title: normal pregancy  [ESC69-P1]

label_protocol: Standard Applied Biosystems FlashTag Biotin HSR RNA Labeling Kits protocol


title: spontaneous miscarriage (IUFD) [ESC44-P1]

status: Public on May 20 2024

type: RNA

city: TauYau

first: Yun-Shien

last: Lee

state: Taiwan

address: TauYau

department: Dept. Biotechnology

country: Taiwan

institute: Ming Chuan Univ

description: miRNA expression data from spontaneous miscarriage(IUFD)

hyb_protocol: Standard Applied Biosystems FlashTag Biotin HSR RNA Labeling Kits protocol

data_processing: Normalize with Experssion(Gene) RMA+DABG (Human Only) by Applied Biosystems Transcriptome Analysis Console Ver 4.0

label: biotin

molecule: total RNA

organism: Homo sapiens

source_name: spontaneous miscarriage (IUFD)

growth_protocol: human decidual stromal cells were isolated from the decidual tissue(normal pregnancy and spontaneous miscarriage ).

extract_protocol: Exosomes used for RNA extraction were resuspended inTRI Reagent LS and protocol as detailed by manufacturer.

treatment_protocol: Extracellular vesicles were extracted from human decidual stromal cells  in media with FBS depleted of extracellular vesicles .

tag: subject status

value: spontaneous miscarriage (IUFD)

tag: cell type

value: human decidaul stromal cells

value: primary cells


title: Tumor adjacent tissue of patient 9

type: SRA

city: Nanning

first: Wenyu

last: Feng

state: Guangxi

address: Shuangyong road 22

department: Center for Genomic and Personalized Medicine

country: China

institute: Guangxi Medical University

library_source: transcriptomic single cell

data_processing: Processed data details to be added at a later date.

source_name: Tumor adjacent tissue

extract_protocol:
Immediately after surgical excision to remove the tumor, we collected fresh samples and placed them in an ice solution containing Hank's balanced salt solution and 1% antifungal antibody, and transferred the tissue into a 4 ℃refrigerator for storage within 20 minutes. Subsequently, a small soft tissue sample was taken and cut into 1 mm3 pieces, washed well using DPBS (cat. no. C14190500BT; Thermo Fisher Scientific, Inc.), and digested by adding collagenase 2 (1 mg/mL) for 45 min at 37 ℃. The cells were filtered using a 100 uM cell filter, and the obtained cell suspension was centrifuged for 5 min at 300 g. The supernatant was removed, and red blood cells were removed using 1× red blood cell lysis buffer (10× diluted to 1×; cat. no. B250015; BioLegend, Inc.). Finally, after washing the cells with PBS, the cells were resuspended using BPBS. Meanwhile, cell viability will be assessed using 0.4% Trypan blue staining.
Paracancerous tissues contain more hard bone composition, which presents great challenges in single-cell sequencing. To overcome this limitation, in this study, we first used αMEM (SH30265.01, HyClone) to clean the hard bone three times and bite them into small pieces of about 1-2 mm in diameter. 12 ml of collagenase type II at a concentration of 2 mg/ml (Cat: A004174-0001, Sangon Biotech) was mixed with αMEM containing 100 U/ml penicillin and 100 μg/ml streptomycin (Cat:15140-122, Gibco) in a 50 ml conical tube. The bone snap was then placed in it and digested at 37 °C for 25 min with gentle agitation. Afterwards, the collagenase solution was removed aseptically and the bone pieces were rinsed three times in 10 ml of PBS. After five rounds of digestion, the collagenase solutions from the last two rounds of digestion were combined and the solutions were filtered through a 40 μm filter. Finally, Red Blood Cell Lysis Solution (10×) was used to remove red blood cells according to the manufacturer's instructions.
The final single cells from each sample were loaded on a 10× Genomics Chromium Single-Cell Chip along with the single cell master mix and single cell 3’ gel beads (10× Genomics) to generate single-cell gel bead-in-emulsions (GEMs). According to the manufacturer’s instructions the samples were processed by 10× Genomics V3 barcoding chemistry kits. mRNA in drops were undergo the reverse transcription reactions and then the cDNA amplification was followed by the instructions. And the single cell libraries were sequenced on an Illumina NovaSeq 6000 instrument.

tag: subject

value: patient 9

tag: tissue

value: Tumor adjacent tissue


title: spontaneous miscarriage (Blighted ovum) [ESC63]

description: miRNA expression data from spontaneous miscarriage(Blighted ovum)

scan_protocol: Standard Applied Biosystems FlashTag Biotin HSR RNA Labeling Kits protocol

source_name: spontaneous miscarriage (Blighted ovum)

value: spontaneous miscarriage (Blighted ovum)


title: UKN1_SBAD2_Butylparaben_1_3

city: Dortmund

first: Jan

middle: Georg

last: Hengstler

address: Ardeystraße 67

department: Toxikologie / Systemtoxikologie

country: Germany

institute: Leibniz-Institut für Arbeitsforschung an der TU Dortmund

hyb_protocol: The samples were purified using magnetic beads and fragmented. 12,5 μg of fragmented RNA samples were hybridized on Affymetrix Human Genome U133 Plus 2.0 arrays (Affymetrix, Santa Clara, CA, USA). The microarray hybridization step was performed in an Affymetrix GeneChip Hybridization Oven-645 for 16 h at 45 °C and 60 rpm. Washing and staining of the hybridized arrays was completed using the GeneChip HWS Kit (Affymetrix, High Wycombe, United Kingdom) and Affymetrix GeneChip Fluidics Station-450.

scan_protocol: Stained arrays were scanned with Affymetrix Gene-Chip Scanner-3000-7G and evaluated for quality control with Affymetrix GCOS software

data_processing: All analyses were conducted using the statistical software R, version 4.2.1 Pre-processing of the data consists of the three steps background correction, normalization, and summarization, using the frozen robust multi-array average (fRMA) algorithm. This yields expression values for 54675 probe sets. The R-packages affy, frma and hgu133plus2frmavecs were used.

source_name: SBAD2 iPS cells

label_protocol: The samples were amplified and labelled with biotin using GeneChip 3′ IVT Express Kit per the manufacturer’s instructions (Affymetrix, High Wycombe, UK).

growth_protocol: The differentiation of SBAD2 hiPSCs to neuroepithelial precursor cells was performed using the UKN1 protocol (Chambers et al. 2009) with minor changes. Briefly, hiPSCs were seeded in 1 ml pluripotent stem cell (PSC) medium (spiked with a Rho-kinase inhibitor (ROCKi)) per well on extracellular matrix protein-coated 12-well-plates at a density of 12,000 - 24,000 cells/cm² on day -3. On day  2 and day  1, the PSC medium was refreshed. On days 0, 1 and 2, medium was changed to differentiation medium, which was spiked with 21.6 µM SB431542, 0.64 µM dorsomorphin, 35 ng/ml noggin and 0.1% DMSO to induce neural differentiation. On day 4, medium was changed to a mixed medium of 75% differentiation medium / 25% N2-S and the same concentrations of SB431542, dorsomorphin and noggin as given above. On day 6, cells were collected for RNA extraction. A more detailed method description is given in the supplemental information.

extract_protocol: Total RNA was isolated from sonicated cell lysates with the ExtractMe Total RNA-Kit (Blirt, Poland). The concentration and purity of the RNA were determined with a NanoDrop2000 (ThermoFisher Scientific, Germany).

treatment_protocol: On days 0, 1 and 2, differentiating cells were incubated (5% CO2, 37 °C) with paraben concentrations ranging from 0.316 – 1000 µM and valproic acid at 600 µM for a total of 96 h, as well as the vehicle alone (0.1% DMSO).

value: SBAD2 iPS cells

tag: Sex

value: male


title: UKN1_SBAD2_Butylparaben_1_1


title: UKN1_SBAD2_Butylparaben_3.16_2


title: AMC-86-post

city: New York

first: Aarthi

last: Ramakrishnan

state: New York

address: 1425 Madison Avenue

department: Neuroscience

country: USA

institute: Icahn School of Medicine at Mount Sinai

library_source: transcriptomic

data_processing:
Data were aligned to mm10 genome and filtered for low abundance transcripts by keeping only genes expressed at CPM ≥5 in at least 85% of samples before further analysis.
After filtering, pair-wise differential expression comparisons using DEseq2 were performed to identify differentially expressed genes (DEGs) in comparisons of pre- and post-resilient vs control and susceptible vs control and a nominal significance threshold of fold change>2 and p<0.025 was applied.
Genome_build: mm10
Supplementary_files_format_and_content: Tab-delimited text file

organism: Mus musculus

source_name: Sperm

extract_protocol:
Total RNA was isolated from frozen mature sperm from adult male mice using a protocol combining TRIzol/chloroform extraction with RNeasy MiniElute Cleanup kit. In short, 200 µl Trizol was used to homogenize the tissue. An additional 500 µl Trizol was added along with 140 µl chloroform. The lysate was centrifuged at 12,000xg for 15 minutes and the aqueous layer was removed and added to the RNeasy mini spin column. The rest of the protocol was completed as outlined by the manufacturer. Samples were treated with DNAse to rid samples of genomic DNA. After extraction, purity and concentration were measured on an Agilent 2100 Bioanalyzer (Agilent, Santa Clara CA) using an RNA 6000 Nano assay.
Libraries were prepared using the TruSeq Stranded Total RNA Library Prep Gold protocol (Illumina, San Diego, CA). Briefly, cDNA was synthesized from ribo-depleted RNA, followed by end-repair and ligation with sequencing adaptors. The libraries were then size selected and purified using AMPure XP beads (Beckman Coulter, Brea, CA). Barcode bases (8 bp) were introduced at one end of the adaptors during PCR amplification steps. Library size and concentration were measured by Bioanalyzer or Tape Station (Life Technologies, Grand Island, NY) before sequencing. All libraries were pooled for multiplexing and sequenced on the Illumina HiSeq 2500 System utilizing V3 chemistry with 150 base pair double-end reads at the sequenced on a HighSeq2500 System using V4 chemistry with 50 base pair single-end reads at GeneWiz LLC (South Plainfield, NJ).

tag: surgery group

value: Control

tag: treatment

value: Defeat

tag: si group

value: Susceptible

tag: sperm time point

value: Sperm


title: AMC-90-post

value: Resilient


title: Lymph node tissue of patient 8

source_name: Lymph node tissue

value: patient 8

value: Lymph node tissue


title: UKN1_SBAD2_Butylparaben_1_2


title: spontaneous miscarriage (IUFD) [ESC35]


title: UKN1_SBAD2_Butylparaben_0.316_3


title: UKN1_SBAD2_Butylparaben_0.316_1


title: daf2_whole worm_rep 3

city: Valhalla

first: Jian

last: Li

state: NY

address: 15 Dana Road

institute: New York Medical College

data_processing:
RNA-seq reads were mapped to Ensembl WBcel235 genome using RNA STAR (Dobin et al., 2013) with --alignIntronMax 120000 to set the intron size, and --outFilterMultimapNmax 200 to allow multi-mapped reads. All paired-end reads were trimmed to 50 bp to make downstream mapping and analyses consistent.
The mapped reads were then subject to FeatureCounts in Rsubread (Liao et al., 2019) for quantification with the setting -p -B -P -C -M -O --fraction –largestOverlap. The settings in STAR and FeatureCounts enabled proper quantification of those heat shock genes (e.g. hsp-70 and hsp-16s) that are duplicated in C. elegans genome.
Differential expression (DE) analyses were then done using edgeR (Robinson et al., 2010) with default settings except of using Likelyhood Ratio Test and filtering out those lowly expressed genes with CPM (counts per million) value less than 1 in more than 75% samples. We then filtered out DE genes that were caused by auxin treatment using a list from our previous study (Edwards et al 2021) and reported only DE genes caused by HSF-1 depletion.
Assembly: WS235/ce11
Supplementary files format and content: edgeR_norncounts: excel files containing normalized expression in log2 CPM (counts per million reads)
Supplementary files format and content: edgeR_DE: excel files containing differential expression analysis on altered gene expression caused by HSF-1 depletion or by reduced insulin/IGF-1 signaling in the germline nuclei

molecule: polyA RNA

organism: Caenorhabditis elegans

source_name: whole animal

growth_protocol: C. elegans strains were maintained at 20°C on NGM plates seeded with OP50 bacteria and were handled using standard techniques. Animals were synchronized by treatment of alkaline hypochlorite solution or egg laying (for auxin treatment starting from egg lay).

extract_protocol:
RNA was extracted using 300 uL Trizol reagent. Worms were vortexed continuously for 20 minutes at 4C and then went through one cycle of freeze-thaw to help release RNA. Following this, RNA was purified using the Direct-zol RNA MiniPrep kit (Zymo Research) per the manufacturer’s instructions using on-column DNase I digestion to remove genomic DNA.
Total RNAs were polyA enriched, and directional RNA-seq libraries were prepared using NEBNext Ultra II RNA library prep Kit.

treatment_protocol: For HSF-1 depletion from the germline, animals were either egg lay onto the plates containing 1 mM auxin or 0.25% EtOH as a negative control, or transferred onto auxin and EtOH plates at the young-adult stage and kept for 16 hours. For germline nuclei isolation, we followed a published protocol (Han et al 2019) except that worms were lightly fixed in 50 mL of −20°C dimethylformamide (Sigma-Aldrich) for 2 min and washed three times in PBS before homogenization. This light fixation helped preserve the RNA from degradation.

value: whole animal

tag: genotype

value: whole worm lysate


title: UKN1_SBAD2_Butylparaben_0.316_2


title: AMC-84-post


title: Tumor adjacent tissue of patient 8


title: AMC-79-post


title: I1FT

city: Beijing

first: Qiang

last: Sun

state: Beijing

address: 20 Dongda Street

department: Laboratory of Cell Engineering

institute: Institute of Biotechnology

hyb_protocol: DNA in hybridization solution was denatured at 95℃ for 3 min prior to loading onto a microarray. Arrays were hybridized was performed in a Agilent Hybridization Oven overnight at a rotation speed of 20 rpm at 42℃ and washed with two consecutive solutions (0.2% SDS, 2× SSC at 42℃ for 5 min, and 0.2× SSC for 5 min at room temperature).

scan_protocol: Scanned on an Agilent G2565CA scanner.

data_processing: Feature Extraction v10.7 (Agilent Technologies, CA) software was used to extract all features of the data obtained from the scanned images and GeneSpring software was used to analyze the raw data, which are normalized by percentile normalization.

source_name: Liver tumor cell

label_protocol: cDNA labeled with a fluorescent dye (Cy3-dCTP) was produced by Eberwine’s linear RNA amplification method and subsequent enzymatic reaction. This procedure has been previously described, and the procedure has been improved by using CapitalBio cRNA Amplification and Labeling Kit (CapitalBio) for producing higher yields of labeled cDNA.

growth_protocol: Cell line PLC/PRF/5 and its derivatives were routinely maintained in Dulbecco’s modified Eagle’s medium (MACGENE Technology Ltd., Beijing, China) supplemented with 10% fetal bovine serum (Kangyuan Biology, China), and 100 units/mL penicillin plus 100 µg/mL streptomycin (Invitrogen).

extract_protocol: RNA was prepared using the TRIzol reagent following the manufacturer's recommendations. RNA was quantified using a NanoDrop-1000 spectrophotometer.

tag: cell line

value: Untreated


title: daf2_germline nuclei_rep 3

source_name: germline

value: germline

value: enriched germline nuclei


title: G4FT


title: Primary osteosarcoma tissues of patient 8

source_name: Primary osteosarcoma tumor tissue

value: Primary osteosarcoma tumor tissue


title: wildtype_germline nuclei_rep 3


title: Lymph node tissue of patient 7

value: patient 7


title: AMC-72-post


title: I7S


title: daf2_whole worm_rep 2


title: daf2_germline nuclei_rep 2


title: Tumor adjacent tissue of patient 7

value: Tumor adjacent tissue


title: Primary osteosarcoma tissues of patient 7


title: wildtype_whole worm_rep 2


title: AMC-70-post

value: Surgery


title: wildtype_germline nuclei_rep 2


title: 5-8SCFAJEV24hpi_R1

city: Gurugram

first: Anirban

last: Basu

state: Haryana

address: Nainwal Mor, Manesar

department: Cellular and molecular neuroscience

country: India

institute: National Brain Research Centre

library_source: other

data_processing:
Quality check of the data was performed using FastQC v0.11.9 and MultiQC v1.9 software.
Trimgalore v0.6.6 and Cutadapt v3.4 programs were used to remove adaptor sequencesand low quality bases
sequencing data were mapped onto indexed Mouse reference genome (GRCm38) using mapper.pl script of miRDeep2 v2.0.1.2.
Assembly: GRCm38
Supplementary files format and content: Expression counts and normalized expression counts in xlsx files

molecule: other

growth_protocol: N9 microglial cells were grown and maintained in DMEM substituted with 10% FBS and 100units/mL of penstrap in humidified atmosphere at 37 degrees celcius and 5% CO2

extract_protocol:
Total RNA was extracted using phenol-chloroform method The RNA pellet was dissolved in RNase free water and rRNA depletion was performed using 1 μg of total RNA and further used for library preparation.
NEBNext® Ultra™ II Directional RNA Library Prep Kit was used to prepare RNA-seq libraries according to manufacturer's protocol

treatment_protocol: N9 cells were pretretaed with SCFA cocktail for 12 hours, followed by 2hrs serum starvation and incubation in JEV containing medium for 2 hrs. Thereafter the cells were transferred to mainatence media and collected 6 hours and 24 hours post infection.

value: Microglia

value: SCFA cocktail+JEV infection

tag: time point


title: AMC-69-pre


title: Uninfected_Colon-organoid_3

city: Minato-ku

first: Kei

last: Sato

state: Tokyo

address: 4-6-1 Shiroganedai

department: Department of Microbiology and Immunology

country: Japan

institute: The Institute of Medical Science, The University of Tokyo

data_processing:
Sequenced reads were trimmed with fastp (v.0.21.0).
Sequenced reads were mapped to the human, SARS-CoV-2, and BANAL-236 reference genomes using STAR (v.2.6.1c).
Assembly: Human (GRCh38.p13), BANAL-236 (MZ937003.2), and SARS-CoV-2 (NC_045512.2)
Supplementary files format and content: Expression read count matrix (counts.txt)

source_name: iPSC-derived colon organoid

extract_protocol:
Total RNA was extracted using QIAamp RNA Blood Mini Kit (Qiagen, Cat# 52304)
RNA libraries for RNA-seq were prepared using TruSeq  Stranded mRNA Library Prep Kit (illumina) following manufacturer's protocols.

value: iPSC-derived colon organoid


title: G6F


title: AMC-75-post

value: Control

value: Defeat


title: F6FT


title: AMC-69-post

value: Sperm


title: F1F


title: E2T


title: E18F


title: Uninfected_Colon-organoid_1


title: 5-6SCFAControl24hpi_R1

value: SCFA cocktail


title: AMC-70-pre


title: C1FT


title: daf2_germline nuclei_rep 1


title: AMC-68-pre


title: 5-5Control24hpi_R1

value: No treatment


title: A4S


title: AMC-68-post


title: wildtype_whole worm_rep 1

value: whole animal


title: WK-521_Colon-organoid_2


title: WK-521_Colon-organoid_3


title: wildtype_whole worm_rep 3

value: whole worm lysate


title: 5-4SCFAJEV6hpi_R1


title: wildtype_germline nuclei_rep 1


title: 5-7JEVControl24hpi_R1

value: JEV infection


title: AMC-67-pre


title: WK-521_Colon-organoid_1


title: daf-2_HSF-1 depletion_egg_88h_rep 3

value: Auxin


title: Uninfected_Colon-organoid_2


title: 5-2-SCFACONTROL6hpi_R1


title: daf2_whole worm_rep 1


title: 5-3JEVControl6hpi_R1


title: WK-521-delFCS_Colon-organoid_3


title: AMC-66-pre


title: WK-521-delFCS_Colon-organoid_2


title: daf-2_control_egg_88h_rep 3

value: EtOH


title: daf-2_HSF-1 depletion_egg_88h_rep 2


title: WK-521-delFCS_Colon-organoid_1


title: daf-2_control_egg_88h_rep 2


title: AMC-61-post


title: BANAL-20-236_Colon-organoid_3


title: 4-7JEVControl24hpi_R1


title: daf-2_HSF-1 depletion_egg_88h_rep 1


title: AMC-61-pre


title: AMC-59-pre

value: Resilient


title: AMC-67-post


title: BANAL-20-236_Colon-organoid_2


title: AMC-59-post


title: 4-5Control24hpi_R1


title: 4-4SCFAJEV6hpi_R1


title: daf-2_control_egg_88h_rep 1


title: daf-2_HSF-1 depletion_YA_16h_rep 3


title: BANAL-20-236_Colon-organoid_1


title: Uninfected_HiLung-Airway_4

source_name: iPSC-derived airway cell

value: iPSC-derived airway cell


title: 4-3JEVControl6hpi_R1


title: AMC-57-pre

value: Susceptible


title: 4-8SCFAJEV24hpi_R1


title: Uninfected_HiLung-Airway_3


title: 4-6SCFAControl24hpi_R1


title: daf-2_HSF-1 depletion_YA_16h_rep 2


title: 5-1Control6hpi_R1


title: AMC-66-post

value: Surgery


title: AMC-57-post


title: 4-2-SCFACONTROL6hpi_R1

value: Microglia


title: Uninfected_HiLung-Airway_2


title: daf-2_control_YA_16h_rep 3


title: AMC-55-pre


title: 4-1Control6hpi_R1


title: daf-2_control_YA_16h_rep 2


title: AMC-55-post


title: daf-2_HSF-1 depletion_YA_16h_rep 1


title: 3-8SCFAJEV24hpi_R1

value: SCFA cocktail+JEV infection


title: AMC-54-pre


title: WK-521-delFCS_HiLung-Airway_4


title: daf-2_control_YA_16h_rep 1


title: 3-7JEVControl24hpi_R1


title: WK-521-delFCS_HiLung-Airway_3


title: AMC-54-post


title: AMC-52-pre


title: SEV S3_Input

city: shanghai

first: yanyong

last: cheng

address: 639 Zhizaoju Road

department: Department of Anesthesiology

institute: Shanghai Ninth People's Hospital Affiliated to Shanghai Jiao Tong University School of Medicine

data_processing:
Library strategy: MeRIP-seq
Raw data filtration, low quality bases were trimmed by using Trim Galore (version: 0.5.0). Adapter sequences which are illumina True-seq adapter sequences were trimmed by using cutadapt implemented in Trim Galore.
Alignment，clean reads were mapped to genome (rheMac8) using hisat2 (version:2.1.0) with default parameters.
Peak calling and Differential peak detection，the R package exomePeak (version: 2.1.2) was used to call peaks and detect differential peaks from filtered alignment files with parameters that "WINDOW_WIDTH=200 SLIDING_STEP=30 FRAGMENT_LENGTH=150 DIFF_PEAK_ABS_FOLD_CHANGE=2 FOLD_ENRICHMENT=2". Only peaks with FDR < 0.05 and foldchange >=2 were identified as being significantly differential peaks.
Generation of normalized abundance measurements, gene expression calculation was performed by StringTie software using default parameters. Gene expression profiling was based on the number of reads. TPM ( Transcripts Per Million mapped reads) values were used to estimate the expressed values and transcript levels.
Genome_build: rheMac8
Supplementary_files_format_and_content: Peak calling: tab-delimited text files include Peak Enrichment values for each sample;

organism: Macaca mulatta

source_name: prefontal cortex from sevoflurane rhesus macaques

growth_protocol: The tissues samples of prefrontal cortex were surgically removed and total RNA of the tissues was extracted using TRIzol reagent (Invitrogen, USA).

extract_protocol:
Total RNA was extracted using TRIzol reagent (Invitrogen, USA). Approximately 20 μg of total RNA from each sample was fragmented,and RNA fragments incubated with the m6A antibody-  Protein A/G magnetic beads.
The MeRIP libraries using eluted RNA were constructed using SMARTer Stranded Total RNA-Seq Kit version 2 (Takara/Clontech) according to the manufacturer’s protocol. Briefly, the eluted m6A RNA and input RNA were directly conducted first-strand cDNA synthesis without fragmentation. After that, all following steps were based on the manufacture of the SMARTer Stranded Total RNA-Seq Kit version 2. Libraries for IP RNA were PCR amplified for less than 16 cycles and input libraries were less than 12 cycles. All libraries were analyzed by an Agilent 2100 Bioanalyzer (Agilent Technologies) and quantified by real time PCR before sequencing.

treatment_protocol: Rhesus macaque were exposed to about 2.5%-3% sevoflurane  inhalation anesthesia on approximately postnatal day 7 and then again 21  and 35 days, for four hours each time.

value: F

value: prefontal cortex

tag: age (postnatal day)

value: sevoflurane


title: 3-5Control24hpi_R1


title: SEV S3_IP


title: 3-6SCFAControl24hpi_R1


title: AMC-52-post

value: Defeat

value: Sperm


title: 3-4SCFAJEV6hpi_R1


title: SEV S2_IP


title: BANAL-20-236_HiLung-Airway_4


title: AMC-51-pre


title: WK-521-delFCS_HiLung-Airway_1


title: 3-3JEVControl6hpi_R1


title: SEV S2_Input


title: BANAL-20-236_HiLung-Airway_3


title: SEV S1_IP

value: M


title: Uninfected_HiLung-Airway_1


title: 3-2-SCFACONTROL6hpi_R1

value: SCFA cocktail


title: BANAL-20-236_HiLung-Airway_2


title: 3-1Control6hpi_R1

value: No treatment


title: SEV S1_Input


title: AMC-49-pre


title: AMC-48-post


title: SEV F_IP


title: SEV D_IP


title: WK-521_HiLung-Airway_4


title: WK-521_HiLung-Airway_1


title: WK-521-delFCS_HiLung-Airway_2


title: DSI-treated HEE passage 6 rep 3

city: Cleveland

first: Ann

last: Harris

state: OH

address: 2109 Adelbert Rd

department: Department of Genetics and Genome Sciences

institute: Case Western Reserve University

data_processing:
Sequences were mapped to the hg19 human genome with STAR 2.7 (https://github.com/alexdobin/STAR)
Aligned reads were assigned to genomic features with featureCounts version 1.6.3 in the Subread package (http://subread.sourceforge.net/) to estimate expression levels for each transcript.
Differential gene expression was analyzed using DEseq2 version 1.22.1 (https://www.bioconductor.org/packages/release/bioc/html/DESeq2.html). Samples were normalized and expressed as DESEQ2 normalized counts and both a test statistic (P-value) and an adjusted P-value (q-value) were calculated.
Normalized counts were subjected to principal component analysis
Gene ontology analysis was performed using GO terms database on R
Assembly: hg19
Supplementary files format and content: Excel files include normalized count values for each Sample

source_name: Head (caput) epididymis

growth_protocol: HEE cells were cultured in Primaria flasks in their regular media (CMRL1066 medium with 15% FBS, 2 mmol/L L-glutamine, 1 mg/mL hydrocortisone, 0.2 U/mL insulin, and 10-10 mol/L cholera toxin (Non treated)) or in the same media to which small molecule cocktail (1µM A-8301, 1µM DMH-1, 1µM CHIR99021, and 5 µM Y27632, (Dual SMAD inhibited)) was added. Passage 3 or 6 cells were used

extract_protocol:
RNA was extracted from HEE cells using TRIzol. RNA quality was confirmed by Nanodrop measurement of OD 260/280 and 260/230 ratios and by Tapestation.
Oligo-dT mRNA directional

value: Human epididymis epithelial cells

value: DSI

tag: passages


title: Ctrl C3_Input

source_name: prefontal cortex from control rhesus macaques

value: control


title: WK-521_HiLung-Airway_3


title: AMC-47-post

value: Resilient


title: SEV F_Input


title: Ctrl C2_IP


title: WK-521_HiLung-Airway_2

value: iPSC-derived airway cell


title: darrowii_rep2_WGBS

first: Zejia

last: Wang

address: Yanyuan Street

institute: Peking University

library_source: genomic

data_processing:
Adaptors were first trimmed from the raw sequencing reads using fastp v0.20.1. The trimmed reads were aligned to reference genome(2019 gigascience) using BSseeker2  under default. Reads with more than three consecutive methylated CHH were removed as described previously. CGmaptools is used for downstream analysis and visualization
V_corymbosum_v1.0
The processed data is generated  by BSseeker2 and Cgmaptools.
For RNA-seq analysis, adaptors of the raw reads were trimmed off using fastp v0.20.1. The trimmed reads were aligned to the Vaccinium corymbosum cv ‘Draper’ genome using HISAT2 v2.2.1 under default settings. Since “Draper” is tetraploid, we selected largest scaffolds of each of the 12 homoeologous groups to represent the genome. The expression level of each gene, measured as TPM (Transcripts Per kilobase of exon model per Million mapped reads) values, were counted using featureCounts of the Subread package v2.0.2  with default parameters.
V_corymbosum_v1.0
The processed data is generated  by HISAT2

molecule: genomic DNA

organism: Vaccinium darrowii

source_name: leaf

extract_protocol: Blueberry leaves were collected for DNA extraction using a CTAB-based method. 400 ng DNA was used for bisulfite conversion with the EZ DNA methylation-lighting kit

value: leaf

value: wild type

tag: time

value: after flowering


title: Ctrl C3_IP


title: AMC-48-pre

value: Surgery


title: DSI-treated HEE passage 6 rep 2


title: darrowii_rep1_WGBS


title: AMC-49-post


title: AMC-39-pre


title: AMC-47-pre


title: AMC-42-post

value: Susceptible


title: Non treated HEE passage 6 rep 3


title: DSI-treated HEE passage 6 rep 1


title: Ctrl C2_Input

value: F

value: prefontal cortex


title: darrowii_rep3_RNAseq

data_processing:
For RNA-seq analysis, adaptors of the raw reads were trimmed off using fastp v0.20.1. The trimmed reads were aligned to the Vaccinium corymbosum cv ‘Draper’ genome using HISAT2 v2.2.1 under default settings. Since “Draper” is tetraploid, we selected largest scaffolds of each of the 12 homoeologous groups to represent the genome. The expression level of each gene, measured as TPM (Transcripts Per kilobase of exon model per Million mapped reads) values, were counted using featureCounts of the Subread package v2.0.2  with default parameters.
V_corymbosum_v1.0
The processed data is generated  by HISAT2
For RNA-seq analysis, adaptors of the raw reads were trimmed off using fastp v0.20.1. The trimmed reads were aligned to the Vaccinium corymbosum cv ‘Draper’ genome using HISAT2 v2.2.1 under default settings. Since “Draper” is tetraploid, we selected largest scaffolds of each of the 12 homoeologous groups to represent the genome. The expression level of each gene, measured as TPM (Transcripts Per kilobase of exon model per Million mapped reads) values, were counted using featureCounts of the Subread package v2.0.2  with default parameters.
V_corymbosum_v1.0
The processed data is generated  by HISAT2

extract_protocol: The total RNA was isolated from the strain using the Trizol reagent according to manufacturer’s instructions (Invitrogen) and sent to Novogene (Tianjin, China) for library  preparation and deep sequencing.


title: AMC-51-post

value: Defeat


title: BANAL-20-236_HiLung-Airway_1


title: Ctrl C1_IP


title: SEV D_Input

value: sevoflurane


title: AMC-39-post

value: Sperm


title: Non treated HEE passage 6 rep 2


title: AMC-28-pre


title: Ctrl C1_Input


title: MB3

city: guang zhou

first: CaiYun

last: He

address: Yingdong Building, No 96, Dongchuan Road, Yuexiu District, Guangzhou, 510080, People's Republic of China.

institute: Guangdong Provincial People's Hospital

data_processing:
The sequencing data was filtered with SOAPnuke. Afterwards clean reads were obtained and stored in FASTQ format.
Bowtie2 was applied to align the clean reads to the gene set, a database built by BGI (Beijing Genomic Institute in ShenZhen).
Expression level of gene was calculated by RSEM (v1.3.1). Differential expression analysis was performed using the DESeq2(v1.4.5).
The analysis and data mining were performed on Dr. Tom Multi-omics Data mining system.
Assembly: mm9

source_name: bone marrow cells

growth_protocol: BMDMs were induced in RPMI-1640 medium supplemented with 50ng/ml M-CSF, 20% FBS, 1% penicillin/streptomycin at 37℃ and 5% CO2 for 7 days.

extract_protocol:
RNA was extracted from cells via TRIzol reagent.
RNA libraries were prepared for RNA-seq using high-intensity DNA nanochip technique and sequenced through combinatorial Probe-Anchor Synthesis (cPAS).

value: bone marrow cells

value: differentiated into BMDMs with 50ng/ml M-CSF


title: AMC-27-pre


title: AMC-27-post


title: Ctrl C_IP


title: Non treated HEE passage 6 rep 1

value: Human epididymis epithelial cells


title: Ctrl B_IP

value: M


title: AMC-28-post


title: DSI-treated HEE passage 3 rep 2

value: DSI


title: Ctrl C_Input

value: control


title: MB1


title: Non treated HEE passage 3 rep 3


title: Ctrl B_Input


title: WT3

value: Morrbidfl/fl


title: AMC-11-pre


title: AMC-11-post


title: Non treated HEE passage 3 rep 2


title: darrowii_rep2_RNAseq

value: leaf


title: darrowii_rep1_RNAseq

value: wild type


title: AMC-100-post

value: Control


title: Ctrl A _Input


title: MB2


title: WT1


title: DSI-treated HEE passage 3 rep 3


title: Non treated HEE passage 3 rep 1


title: H3K27ac ChIP-seq in ESC after NVP-2 treatment for 120min treatment rep2

status: Public on May 19 2024

city: Copenhagen N

first: Chunarum

last: Choudhary

state: --- Select a state ---

address: Blegdamsvej 3B

department: Novo Nordisk Foundation Center for Protein Research

country: Denmark

institute: University of Copenhagen

description:
Human HEK293 cell was used as spike-in.
ESC_Ctrl_TC0_H3K27ac.ab4729_CC39.CC44_peak.bed
ESC_NVP2_100nM_TC120_H3K27ac.ab4729_spike.HEK293_CC39.CC44.spTotal.norm.smooth.bw
ESC_Ctrl_TC0_H3K27ac.ab4729_CC39.CC44_peak.bed

data_processing:
Adaptors were trimmed using Cutadapt. Read sequences were aligned to the combined mouse mm10 and human hg19 genome using bwa meme (version 1.0.4) with soft clipping option for supplementary alignments. Duplicated reads were annotated and removed using Picard toolkit tools (version 2.9.1, “Picard Toolkit.” 2019. Broad Institute, GitHub Repository. https://broadinstitute.github.io/picard/; Broad Institute). Low-mapping quality reads (MAPQ < 10) were excluded using samtools (version 1.4). Peak calling was conducted using LanceOtron with the default model (wide-and-deep_jan-2021). The peaks proximal within 2kb are merged using Bedtools93.  Peak heights were calculated using bamCompare94 with the following parameters (centerReads, minMappingQuality 10, bin size 20b, smoothing length 400b, extension of reads to 200b, rpm normalization, and input rpm value is subtracted). The peak summit was defined as the center of the 20b bin at maximum height in each peak region. Poorly enriched peaks of maximum peak height at 20bp bin < 8 reads mapped per million (rpm) or read enrichment at +/- 500bp around peak summit center < 1 rpm after input subtraction were excluded. H3K27ac peaks that were not proximal to ATAC-seq peak summit within 400bp, or whose peak summits were more than 1kb from ATAC-seq peak summit were filtered out. The H3K27ac peak changes were quantified by analyzing the read count mapped to peak summit +/- 500bp region. The FC ratios were calculated by using DESeq2 with incorporating scaling factors determined from the HEK293 cell spike-in reads counts.
Assembly: mm10, T2T-CHM13v2.0
Supplementary files format and content: Gene track bigwig files and H3K27ac peak bed file.

source_name: E14 mouse ESC

growth_protocol: E14Tg2A Rosa26-Cre Oct4-IRES-Puro mouse ESCs were used for all experiments (Ying et al., 2002). ESCs were cultured in the standard N2B27 medium consisting of 1:1 mix of DMEM/F12 and Neurobasal medium (Thermo Fisher Scientific), supplemented with 1000 units/ml leukemia inhibitory factor (LIF) (Merck Millipore), 1μM PD0325901, 3μM CT-99021 (custom-made by ABCR GmbH, Karlsruhe), 100μM 2-mercaptoethanol, 150μM sodium pyruvate, 0.5x B27 supplement (Thermo Fisher Scientific), 0.5x N2 supplement (made in house or from Thermo Fisher Scientific.

extract_protocol:
ChIP assay was performed as described previously (Narita et al., 2023) with modifications. mESCs were treated two hours with DMSO, 1 μg/ml Actinomycin D (Tocris Bioscience), or 100 nM NVP2 (Tocris Bioscience), respectively. After treatments, cells were cross-linked with 1% formaldehyde for 10 minutes, neutralized with 0.2 M glycine for 5 minutes, washed twice with PBS, then collected by cell lifter, concentrated as pellets by centrifuged for 10 min at 3000 rpm at 4 °C and stored at -80 °C until use. Cells were resuspended in SDS lysis buffer (10 mM Tris-HCl, pH 8.0, 150 mM NaCl, 1% SDS, 1 mM EDTA, pH 8.0, cOmplete Protease Inhibitor Cocktail (Roche)) and sonicated by a Bioruptor Pico (30 cycles, 30 seconds on and 30 seconds off, Diagenode), then centrifuged for 10 min at 13,000×g at 20 °C for debris removal. The supernatants were stored at -80 °C. The aliquots of the supernatant were 5-fold diluted with ChIP dilution buffer (20 mM Tris-HCl, pH 8.0, 150 mM NaCl, 1 mM EDTA, 1% Triton X-100, cOmplete Protease Inhibitor Cocktail), incubated 20 hours at 65 °C to reverse cross-linking, then treated with 0.2 mg/ml RNase A (Thermo Fisher Scientific) for 30 min at 37 °C and proteinase K (Thermo Fisher Scientific) for 1 hour at 55 °C. Then DNA fragments were isolated by phenol-chloroform extraction and recovered by ethanol precipitation with glycogen (Thermo Fisher Scientific). DNA fragments were quantified by Nanodrop (Thermo Fisher Scientific). The 300 bp average size of DNA was measured by 4200 TapeStation System (Agilent Technologies). For immunoprecipitation, the supernatants equivalent to 100 μg of mESC chromatin DNA combined with 10 μg of chromatin DNA derived from HEK293T as spike-in were incubated with anti-histone H3 acetyl K27 antibody (ab4729 Abcam) conjugated with Dynabeads M-280 sheep anti-Rabbit IgG (Thermo Fisher Scientific) by rotating overnight 4 °C . The immunoprecipitated Protein-DNA complexes were washed with ChIP dilution buffer, wash buffer high-salt (20 mM Tris-HCl, pH 8.0, 500 mM NaCl, 2 mM EDTA, 1% Triton X-100, 0.1% SDS), wash buffer low-salt (10 mM Tris-HCl, pH 8.0, 1 mM EDTA, 250 mM LiCl, 0.5% sodium deoxycholate, 0.5% NP-40) once respectively, washed with TE three times, then eluted with elution buffer (50 mM Tris-HCl, pH 8.0, 10 mM EDTA, 1% SDS). The immunoprecipitated DNAs were reversed cross-link and recovered from the eluates as described above.
ChIP-seq, library was prepared from 20 ng of ChIPed DNA measured by Qubit dsDNA HS Assay (Thermo Fisher Scientific) using the NEBNext Ultra II DNA Library Prep Kit for Illumina (New England Biolabs) according to the manufacturer’s instructions. Adoptor-ligated, U-excisioned DNA was cleaned by AMPure XP beads (Beckman Coulter) amplified by PCR 6 cycles, then cleaned again and size-selectioned (350-400 bp average size measured by Tapestation). 4 nM pooled Library DNAs were sequenced on a NextSeq 2000 Sequencer (Illumina) as single-end 138-bp reads.

treatment_protocol: Cells were treated with DMSO or with either 100nM NVP-2 or 1ug/ml Actinomycin D for 120min.

value: E14 mouse ESC

value: ESC

tag: chip antibody

value: H3K27ac (Abcam, ab4729)

value: NVP-2 100nM for 120min


title: H3K27ac ChIP-seq in ESC after actinomycin D treatment for 120min treatment rep2

description:
Human HEK293 cell was used as spike-in.
ESC_Ctrl_TC0_H3K27ac.ab4729_CC39.CC44_peak.bed
ESC_ActD_800nM_TC120_H3K27ac.ab4729_spike.HEK293_CC39.CC44.spTotal.norm.smooth.bw
ESC_Ctrl_TC0_H3K27ac.ab4729_CC39.CC44_peak.bed

value: Actinomycin D 800nM for 120min


title: DSI-treated HEE passage 3 rep 1


title: H3K27ac ChIP-seq in ESC after NVP-2 treatment for 120min treatment rep1


title: H3K27ac ChIP-seq in ESC rep1

description:
Human HEK293 cell was used as spike-in.
ESC_Ctrl_TC0_H3K27ac.ab4729_CC39.CC44_peak.bed
ESC_Ctrl_TC0_H3K27ac.ab4729_spike.HEK293_CC39.CC44.spTotal.norm.smooth.bw
ESC_Ctrl_TC0_H3K27ac.ab4729_CC39.CC44_peak.bed


title: H3K27ac ChIP-seq in ESC after actinomycin D treatment for 120min treatment rep1


title: Sort-purified (CD8/CD45.1) TCR OT1 CD8 T cells from B16-OVA-GP61 tumors (with TCR SMARTA CD4 T cells) replicate#2 [ATAC]

first: Andrea

last: Schietinger

address: 1275 York Avenue

department: Immunology

institute: Memorial Sloan Kettering Cancer Center

data_processing:
Reads were aligned to the mouse reference genome (version GRCm38) with BWA-backtrack v0.7.17 (Li and Durbin, 2009).
Post-alignment filtering was done with samtools v1.8 and Picard tools v2.18.9 (Li et al., 2009) to remove unmapped reads, improperly paired reads, nonunique reads, and duplicates.
Peaks were called with MACS2 v2.1.1 (Liu, 2014),and peaks with adjusted P values smaller than 0.01 were excluded.
Consensus peak sets were generated for each condition if a peak was found in at least two replicates.
Reproducible peaks from each condition were merged with DiffBind v3.4.11 to create an atlas of accessible peaks, which was used for downstream analyses.
Assembly: GRCm38
Supplementary files format and content: bigWig, narrowPeak
Supplementary files format and content: tab-delimted file containing raw counts per peak per sample

source_name: tumor

extract_protocol:
CD8 T cells were FACS-sorted into FCS containing tubes and after sort 10% DMSO were added, mixed and stored at -80°C until all samples were collected. Profiling of Chromatin was performed by ATAC-seq. Cells were thawed and washed in cold PBS and lysed.
After cell lysis, transposition happened at 42ºC for 45 min. After purification of the DNA with the MinElute PCR purification kit (Qiagen), material was amplified for 5 cycles. Additional PCR cycles were evaluated by real time PCR. Final product was cleaned by Ampure Beads at a 1.5x ratio. Libraries were sequenced on a Hiseq 2500 1T in a 50bp/50bp Paired end run, using the TruSeq SBS Kit v3 (Illumina).  An average of 47x106 paired reads were generated per sample.

value: tumor

value: CD8 T cell


title: Sort-purified (CD8/CD45.1) TCR OT1 CD8 T cells from B16-OVA-GP61 tumors (no TCR SMARTA CD4 T cells) replicate#2 [ATAC]


title: Sort-purified (CD8/CD45.1) TCR OT1 CD8 T cells from B16-OVA-GP61 tumors (with TCR SMARTA CD4 T cells) replicate#1 [ATAC]


title: H3K27ac ChIP-seq in ESC rep2


title: Sort-purified (CD8/CD45.1) TCR OT1 CD8 T cells from B16-OVA-GP61 tumors (no TCR SMARTA CD4 T cells) replicate#3 [ATAC]


title: Ctrl A_IP

value: prefontal cortex


title: Sort-purified (CD8/CD45.1) TCR OT1 CD8 T cells from B16-OVA-GP61 tumors (with TCR SMARTA CD4 T cells) replicate#3

data_processing:
DNA sequencing reads were aligned with default parameters to the mouse reference genome (GRCm38.p6) using STAR v2.6.0c (Dobin et al., 2013).
Gene expression estimates were obtained with featureCounts v1.6.2 using composite gene models (union of the exons of all transcript isoforms per gene) from Gencode (version M17; Liao et al., 2014).
Assembly: GRCm38.p6
Supplementary files format and content: tab-delimted featureCounts file containing raw counts per gene, one for each sample

extract_protocol:
CD8 T cells were FACS-sorted straight into Trizol tube and stored at -80°C until all samples were collected. RNA from sorted cells was extracted using RNeasy mini kit (Qiagen) according to instructions provided by the manufacturer. After ribogreen quantification and quality control of Agilent BioAnalyzer, 6-15 ng of total RNA underwent amplification (12 cycles) using the SMART-seq V4 (Clonetech) ultralow input RNA kit for sequencing. 10ng of amplified cDNA was used to prepare Illumina hiseq libraries with the Kapa DNA library preparation chemistry (Kapa Biosystems) using 8 cycles of PCR. Samples were barcoded and run on a Hiseq 2500 1T in a 50bp/50bp Paired end run, using the TruSeq SBS Kit v3 (Illumina).  An average of 51 million paired reads were generated per sample and the percent of mRNA bases was 62.5% on average.
10ng of amplified cDNA was used to prepare Illumina hiseq libraries with the Kapa DNA library preparation chemistry (Kapa Biosystems) using 8 cycles of PCR. Samples were barcoded and run on a Hiseq 2500 1T in a 50bp/50bp Paired end run, using the TruSeq SBS Kit v3 (Illumina).


title: Sort-purified (CD8/CD45.1) TCR OT1 CD8 T cells from B16-OVA-GP61 tumors (with TCR SMARTA CD4 T cells) replicate#1


title: Sort-purified (CD8/CD45.1) TCR OT1 CD8 T cells from B16-OVA-GP61 tumors (with TCR SMARTA CD4 T cells) replicate#2


title: Sort-purified (CD8/CD45.1) TCR OT1 CD8 T cells from B16-OVA-GP61 tumors (with TCR SMARTA CD4 T cells) replicate#3 [ATAC]


title: Sort-purified (CD8/CD45.1) TCR OT1 CD8 T cells from B16-OVA-GP61 tumors (no TCR SMARTA CD4 T cells) replicate#4


title: Sort-purified (CD8/CD45.1) TCR OT1 CD8 T cells from B16-OVA-GP61 tumors (no TCR SMARTA CD4 T cells) replicate#1 [ATAC]


title: Sort-purified (CD8/CD45.1) TCR OT1 CD8 T cells from B16-OVA-GP61 tumors (no TCR SMARTA CD4 T cells) replicate#1


title: HuH-7, HBV transfected, PAm5Cseq

city: Taipei

first: Kevin

last: Tsai

address: 128 Sec. 2, Academia Rd. Nankang

department: Institute of Biomedical Sciences

institute: Academia Sinica

description: human + HBV (GenBank J02203)

data_processing:
fastx toolkit: fastq_quality_filter -Q33| fastx_clipper -Q33 -v -a [index_sequence] -l 15 -c | fastq_to_fasta -Q33
Aligned to the human genome hg19 using Bowtie 1.2.3: bowtie -p 8 -v 1 -a -m 9 --best --strata --chunkmbs 30000
hg19 non-aligning reads aligned to the HBV ayw genome using Bowtie 1.2.3: bowtie -p 8 -m 2 -v 1 -a --norc --best --strata --chunkmbs 30000
Filtered out all reads that lack a TC mutation
Awk script to generate bed file, columns are "chromosome, start, end, score, strand"
Assembly: Our reordered HBV genome is GenBank #J02203.1 with nucleotides 1818-3182(end) forming the first half, and subsequently joined with nucleotides 1-1937 of J02203.1, thus 1818-1937nt of J02203.1 (which covers the viral terminal repeat) is duplicated on both ends of our reordered HBV genome to better represent the HBV native genomic RNA.
Supplementary files format and content: bed files, aligned to the HBV ayw strain genome

extract_protocol:
PA-m5C-seq (PAR-CLIP done with an m5C RNA targeting antibody)
All samples were processed with the NEB Next small RNA-seq library prep kit for Illumina

value: hepatocyte

value: WT

value: +HBV, +6SG


title: GFP transfected HuH-7, HBV transfected, PAR-CLIP

data_processing:
fastx toolkit: fastq_quality_filter -Q33| fastx_clipper -Q33 -v -a [index_sequence] -l 15 -c | fastq_to_fasta -Q33
Aligned to the human genome hg19 using Bowtie 1.2.3: bowtie -p 8 -v 1 -a -m 9 --best --strata --chunkmbs 30000
hg19 non-aligning reads aligned to the HBV ayw genome using Bowtie 1.2.3: bowtie -p 8 -m 2 -v 1 -a --norc --best --strata --chunkmbs 30000
Filtered out all reads that lack a TC mutation
Awk script to generate bed file, columns are "chromosome, start, end, score, strand"
Assembly: Our reordered HBV genome is GenBank #J02203.1 with nucleotides 1818-3182(end) forming the first half, and subsequently joined with nucleotides 1-1937 of J02203.1, thus 1818-1937nt of J02203.1 (which covers the viral terminal repeat) is duplicated on both ends of our reordered HBV genome to better represent the HBV native genomic RNA.
Supplementary files format and content: bed files, aligned to the HBV ayw strain genome
Library strategy: PAR-CLIP

extract_protocol: All samples were processed with the NEB Next small RNA-seq library prep kit for Illumina

value: +HBV+FLAG-GFP


title: HPNE_Kras_day5_sc130

city: Houston

first: Chenghang

last: Zong

state: TX

address: 1 Baylor Plaza

institute: Baylor College of Medicine

data_processing:
The fastq files of read 1 were mapped to the reference transcriptome by using STAR.
The reads were assigned to exon regions or intron regions by using htseq-count.
The UMI sequences were extracted from read 2 (the first five bases).
The reads with the same UMI were collapsed. The number of UMIs of each gene were counted by exon fragments and intron fragments respectively.
Assembly: hg19
Supplementary files format and content: Tab-separated UMI count matrix (exon based); Files: HPNE_KRAS_exon_UMI_count_matrix.txt
Supplementary files format and content: Tab-separated UMI count matrix (intron based); Files: HPNE_KRAS_intron_UMI_count_matrix.txt

source_name: hTERT-HPNE

extract_protocol:
Cells are trypsinized and resuspended in PBS. Single cells are sorted into 96-well plate by FACS.
Libraries were constructed by following snapTotal-seq protocol.

value: hTERT-HPNE

value: KRASG12D overexpression, day5


title: AMC-42-pre

value: Surgery

value: Defeat

value: Susceptible

value: Sperm


title: NSUN2-KO HuH-7, HBV transfected, PAm5Cseq

data_processing:
fastx toolkit: fastq_quality_filter -Q33| fastx_clipper -Q33 -v -a [index_sequence] -l 15 -c | fastq_to_fasta -Q33
Aligned to the human genome hg19 using Bowtie 1.2.3: bowtie -p 8 -v 1 -a -m 9 --best --strata --chunkmbs 30000
hg19 non-aligning reads aligned to the HBV ayw genome using Bowtie 1.2.3: bowtie -p 8 -m 2 -v 1 -a --norc --best --strata --chunkmbs 30000
Filtered out all reads that lack a TC mutation
Awk script to generate bed file, columns are "chromosome, start, end, score, strand"
Assembly: Our reordered HBV genome is GenBank #J02203.1 with nucleotides 1818-3182(end) forming the first half, and subsequently joined with nucleotides 1-1937 of J02203.1, thus 1818-1937nt of J02203.1 (which covers the viral terminal repeat) is duplicated on both ends of our reordered HBV genome to better represent the HBV native genomic RNA.
Supplementary files format and content: bed files, aligned to the HBV ayw strain genome
Library strategy: PA-m5C-seq

value: NSUN2 knockout

value: +HBV


title: NSUN2-transfected HuH-7, HBV transfected, PAR-CLIP


title: HPNE_Kras_day5_sc128


title: HPNE_Kras_day5_sc125


title: HPNE_Kras_day5_sc127


title: WT2

value: bone marrow cells

value: Morrbidfl/fl

value: differentiated into BMDMs with 50ng/ml M-CSF


title: HPNE_Kras_day5_sc129


title: HPNE_Kras_day5_sc119


title: CRISPR control HuH-7, HBV transfected, PAm5Cseq

value: non-targeted Cas9 stable line


title: HPNE_Kras_day5_sc120


title: HPNE_Kras_day5_sc126


title: HPNE_Kras_day5_sc124


title: HPNE_Kras_day5_sc115


title: HPNE_Kras_day5_sc122


title: HPNE_Kras_day5_sc123


title: HPNE_Kras_day5_sc113


title: HPNE_Kras_day5_sc116


title: HPNE_Kras_day5_sc121


title: Sort-purified (CD8/CD45.1) TCR OT1 CD8 T cells from B16-OVA-GP61 tumors (no TCR SMARTA CD4 T cells) replicate#3

value: tumor

value: CD8 T cell


title: HPNE_Kras_day5_sc118


title: HPNE_Kras_day5_sc111


title: HPNE_Kras_day5_sc110


title: HPNE_Kras_day5_sc112


title: HPNE_Kras_day5_sc117


title: HPNE_Kras_day5_sc109


title: HPNE_Kras_day5_sc108


title: HPNE_Kras_day5_sc105


title: Sort-purified (CD8/CD45.1) TCR OT1 CD8 T cells from B16-OVA-GP61 tumors (no TCR SMARTA CD4 T cells) replicate#2


title: HPNE_Kras_day5_sc106


title: HPNE_Kras_day5_sc114


title: HPNE_Kras_day5_sc102


title: HPNE_Kras_day5_sc103


title: HPNE_Kras_day5_sc99


title: HPNE_Kras_day5_sc96


title: HPNE_Kras_day5_sc93


title: HPNE_Kras_day5_sc88


title: HPNE_Kras_day5_sc94


title: HPNE_Kras_day5_sc95


title: HPNE_Kras_day5_sc100


title: HPNE_Kras_day5_sc91


title: HPNE_Kras_day5_sc87


title: HPNE_Kras_day5_sc98


title: HPNE_Kras_day5_sc92


title: HPNE_Kras_day5_sc101


title: HPNE_Kras_day5_sc86


title: HPNE_Kras_day5_sc89


title: HPNE_Kras_day5_sc84


title: HPNE_Kras_day5_sc90


title: HPNE_Kras_day5_sc83


title: HPNE_Kras_day5_sc85


title: HPNE_Kras_day5_sc82


title: HPNE_Kras_day5_sc104


title: HPNE_Kras_day5_sc81


title: HPNE_Kras_day5_sc79


title: HPNE_Kras_day5_sc80


title: HPNE_Kras_day5_sc75


title: HPNE_Kras_day5_sc74


title: HPNE_Kras_day5_sc77


title: HPNE_Kras_day5_sc78


title: HPNE_Kras_day5_sc70


title: HPNE_Kras_day5_sc97


title: HPNE_Kras_day5_sc71


title: HPNE_Kras_day5_sc68


title: HPNE_Kras_day5_sc76


title: HPNE_Kras_day5_sc72


title: HPNE_Kras_day5_sc67


title: HPNE_Kras_day5_sc73


title: HPNE_Kras_day5_sc65


title: HPNE_Kras_day5_sc63


title: HPNE_Kras_day5_sc61


title: HPNE_Kras_day5_sc69


title: HPNE_Kras_day5_sc64


title: HPNE_Kras_day5_sc58


title: HPNE_Kras_day5_sc66


title: HPNE_Kras_day5_sc59


title: HPNE_Kras_day5_sc62


title: HPNE_Kras_day5_sc53


title: HPNE_Kras_day5_sc55


title: HPNE_Kras_day5_sc54


title: HPNE_Kras_day5_sc107


title: HPNE_Kras_day5_sc52


title: HPNE_Kras_day5_sc51


title: HPNE_Kras_day5_sc48


title: HPNE_Kras_day5_sc47


title: HPNE_Kras_day5_sc50


title: HPNE_Kras_day5_sc49


title: HPNE_Kras_day5_sc43


title: HPNE_Kras_day5_sc46


title: HPNE_Kras_day5_sc38


title: HPNE_Kras_day5_sc40


title: HPNE_Kras_day5_sc56


title: HPNE_Kras_day5_sc57


title: HPNE_Kras_day5_sc42


title: HPNE_Kras_day5_sc60


title: HPNE_Kras_day5_sc45


title: HPNE_Kras_day5_sc39


title: HPNE_Kras_day5_sc44


title: HPNE_Kras_day5_sc34


title: HPNE_Kras_day5_sc31


title: HPNE_Kras_day5_sc37


title: HPNE_Kras_day5_sc28


title: HPNE_Kras_day5_sc29


title: HPNE_Kras_day5_sc32


title: HPNE_Kras_day5_sc27


title: HPNE_Kras_day5_sc25


title: HPNE_Kras_day5_sc41


title: HPNE_Kras_day5_sc35


title: HPNE_Kras_day5_sc24


title: HPNE_Kras_day5_sc21


title: HPNE_Kras_day5_sc22


title: HPNE_Kras_day5_sc20


title: HPNE_Kras_day5_sc17


title: HPNE_Kras_day5_sc36


title: HPNE_Kras_day5_sc16


title: HPNE_Kras_day5_sc14


title: HPNE_Kras_day5_sc11


title: HPNE_Kras_day5_sc13


title: HPNE_Kras_day5_sc15


title: HPNE_Kras_day5_sc30


title: HPNE_Kras_day5_sc8


title: HPNE_Kras_day5_sc7


title: HPNE_Kras_day5_sc12


title: HPNE_Kras_day5_sc10


title: HPNE_Kras_day5_sc6


title: HPNE_Kras_day5_sc4


title: HPNE_Kras_day5_sc3


title: HPNE_Kras_day5_sc2


title: HPNE_Kras_day5_sc23


title: HPNE_Kras_day5_sc1


title: HPNE_Kras_day3_sc170

value: KRASG12D overexpression, day3


title: HPNE_Kras_day3_sc167


title: HPNE_Kras_day5_sc26


title: HPNE_Kras_day3_sc171


title: HPNE_Kras_day3_sc169


title: HPNE_Kras_day3_sc161


title: HPNE_Kras_day3_sc164


title: HPNE_Kras_day5_sc5


title: HPNE_Kras_day3_sc165


title: HPNE_Kras_day3_sc159


title: HPNE_Kras_day3_sc163


title: HPNE_Kras_day3_sc162


title: HPNE_Kras_day3_sc158


title: HPNE_Kras_day3_sc155


title: HPNE_Kras_day3_sc156


title: HPNE_Kras_day3_sc160


title: HPNE_Kras_day3_sc157


title: HPNE_Kras_day5_sc18


title: HPNE_Kras_day3_sc153


title: HPNE_Kras_day3_sc154


title: HPNE_Kras_day3_sc151


title: HPNE_Kras_day3_sc152


title: HPNE_Kras_day3_sc150


title: HPNE_Kras_day3_sc148


title: HPNE_Kras_day3_sc168


title: HPNE_Kras_day3_sc149


title: HPNE_Kras_day3_sc147


title: HPNE_Kras_day3_sc145


title: HPNE_Kras_day3_sc166


title: HPNE_Kras_day3_sc146


title: HPNE_Kras_day3_sc144


title: HPNE_Kras_day5_sc33


title: HPNE_Kras_day5_sc9


title: HPNE_Kras_day3_sc139


title: HPNE_Kras_day3_sc136


title: HPNE_Kras_day3_sc143


title: HPNE_Kras_day3_sc141


title: HPNE_Kras_day3_sc142


title: HPNE_Kras_day3_sc130


title: HPNE_Kras_day3_sc135


title: HPNE_Kras_day3_sc140


title: HPNE_Kras_day3_sc134


title: HPNE_Kras_day3_sc133


title: HPNE_Kras_day3_sc138


title: HPNE_Kras_day3_sc126


title: HPNE_Kras_day3_sc132


title: HPNE_Kras_day3_sc137


title: HPNE_Kras_day3_sc127


title: HPNE_Kras_day5_sc19


title: HPNE_Kras_day3_sc124


title: HPNE_Kras_day3_sc125


title: HPNE_Kras_day3_sc122


title: HPNE_Kras_day3_sc121


title: HPNE_Kras_day3_sc123


title: HPNE_Kras_day3_sc117


title: HPNE_Kras_day3_sc118


title: HPNE_Kras_day3_sc116


title: HPNE_Kras_day3_sc119


title: HPNE_Kras_day3_sc120


title: HPNE_Kras_day3_sc114


title: HPNE_Kras_day3_sc131


title: HPNE_Kras_day3_sc112


title: HPNE_Kras_day3_sc115


title: HPNE_Kras_day3_sc128


title: HPNE_Kras_day3_sc113


title: HPNE_Kras_day3_sc106


title: HPNE_Kras_day3_sc110


title: HPNE_Kras_day3_sc111


title: HPNE_Kras_day3_sc109


title: HPNE_Kras_day3_sc129


title: HPNE_Kras_day3_sc108


title: HPNE_Kras_day3_sc105


title: HPNE_Kras_day3_sc104


title: HPNE_Kras_day3_sc107


title: HPNE_Kras_day3_sc98


title: HPNE_Kras_day3_sc103


title: HPNE_Kras_day3_sc100


title: HPNE_Kras_day3_sc99


title: HPNE_Kras_day3_sc97


title: HPNE_Kras_day3_sc102


title: HPNE_Kras_day3_sc96


title: HPNE_Kras_day3_sc95


title: HPNE_Kras_day3_sc101


title: HPNE_Kras_day3_sc93


title: HPNE_Kras_day3_sc94


title: HPNE_Kras_day3_sc90


title: HPNE_Kras_day3_sc89


title: HPNE_Kras_day3_sc92


title: HPNE_Kras_day3_sc88


title: HPNE_Kras_day3_sc87


title: HPNE_Kras_day3_sc86


title: HPNE_Kras_day3_sc84


title: HPNE_Kras_day3_sc83


title: HPNE_Kras_day3_sc80


title: HPNE_Kras_day3_sc81


title: HPNE_Kras_day3_sc79


title: HPNE_Kras_day3_sc82


title: HPNE_Kras_day3_sc77


title: HPNE_Kras_day3_sc75


title: HPNE_Kras_day3_sc76


title: HPNE_Kras_day3_sc73


title: HPNE_Kras_day3_sc74


title: HPNE_Kras_day3_sc85


title: HPNE_Kras_day3_sc72


title: HPNE_Kras_day3_sc68


title: HPNE_Kras_day3_sc69


title: HPNE_Kras_day3_sc67


title: HPNE_Kras_day3_sc70


title: HPNE_Kras_day3_sc66


title: HPNE_Kras_day3_sc65


title: HPNE_Kras_day3_sc91


title: HPNE_Kras_day3_sc64


title: HPNE_Kras_day3_sc62


title: HPNE_Kras_day3_sc60


title: HPNE_Kras_day3_sc61


title: HPNE_Kras_day3_sc58


title: HPNE_Kras_day3_sc63


title: HPNE_Kras_day3_sc56


title: HPNE_Kras_day3_sc78


title: HPNE_Kras_day3_sc59


title: HPNE_Kras_day3_sc52


title: HPNE_Kras_day3_sc53


title: HPNE_Kras_day3_sc54


title: HPNE_Kras_day3_sc51


title: HPNE_Kras_day3_sc50


title: HPNE_Kras_day3_sc55


title: HPNE_Kras_day3_sc71


title: HPNE_Kras_day3_sc49


title: HPNE_Kras_day3_sc46


title: HPNE_Kras_day3_sc45


title: HPNE_Kras_day3_sc43


title: HPNE_Kras_day3_sc42


title: HPNE_Kras_day3_sc41


title: HPNE_Kras_day3_sc40


title: HPNE_Kras_day3_sc39


title: HPNE_Kras_day3_sc38


title: HPNE_Kras_day3_sc57


title: HPNE_Kras_day3_sc35


title: HPNE_Kras_day3_sc37


title: HPNE_Kras_day3_sc33


title: HPNE_Kras_day3_sc31


title: HPNE_Kras_day3_sc32


title: HPNE_Kras_day3_sc36


title: HPNE_Kras_day3_sc29


title: HPNE_Kras_day3_sc30


title: HPNE_Kras_day3_sc28


title: HPNE_Kras_day3_sc26


title: HPNE_Kras_day3_sc25


title: HPNE_Kras_day3_sc27


title: HPNE_Kras_day3_sc24


title: HPNE_Kras_day3_sc23


title: HPNE_Kras_day3_sc48


title: HPNE_Kras_day3_sc47


title: HPNE_Kras_day3_sc44


title: HPNE_Kras_day3_sc21


title: HPNE_Kras_day3_sc22


title: HPNE_Kras_day3_sc19


title: HPNE_Kras_day3_sc18


title: HPNE_Kras_day3_sc17


title: HPNE_Kras_day3_sc16


title: HPNE_Kras_day3_sc14


title: HPNE_Kras_day3_sc20


title: HPNE_Kras_day3_sc15


title: HPNE_Kras_day3_sc34


title: HPNE_Kras_day3_sc11


title: HPNE_Kras_day3_sc9


title: HPNE_Kras_day3_sc13


title: HPNE_Kras_day3_sc10


title: HPNE_Kras_day3_sc7


title: HPNE_Kras_day3_sc5


title: HPNE_Kras_day3_sc8


title: HPNE_Kras_day3_sc6


title: HPNE_Kras_day3_sc4


title: HPNE_Kras_day3_sc3


title: HPNE_Kras_day2_sc170

value: KRASG12D overexpression, day2


title: HPNE_Kras_day3_sc1


title: HPNE_Kras_day2_sc166


title: HPNE_Kras_day2_sc168


title: HPNE_Kras_day2_sc169


title: HPNE_Kras_day2_sc165


title: HPNE_Kras_day2_sc163


title: HPNE_Kras_day2_sc164


title: HPNE_Kras_day2_sc167


title: HPNE_Kras_day2_sc162


title: HPNE_Kras_day2_sc160


title: HPNE_Kras_day2_sc159


title: HPNE_Kras_day3_sc12


title: HPNE_Kras_day2_sc156


title: HPNE_Kras_day2_sc157


title: HPNE_Kras_day2_sc155


title: HPNE_Kras_day2_sc158


title: HPNE_Kras_day2_sc153


title: HPNE_Kras_day2_sc152


title: HPNE_Kras_day2_sc154


title: HPNE_Kras_day2_sc151


title: HPNE_Kras_day3_sc2


title: HPNE_Kras_day2_sc148


title: HPNE_Kras_day2_sc150


title: HPNE_Kras_day2_sc149


title: HPNE_Kras_day2_sc146


title: HPNE_Kras_day2_sc145


title: HPNE_Kras_day2_sc144


title: HPNE_Kras_day2_sc147


title: HPNE_Kras_day2_sc142


title: HPNE_Kras_day2_sc140


title: HPNE_Kras_day2_sc161


title: HPNE_Kras_day2_sc143


title: HPNE_Kras_day2_sc139


title: HPNE_Kras_day2_sc138


title: HPNE_Kras_day2_sc137


title: HPNE_Kras_day2_sc141


title: HPNE_Kras_day2_sc135


title: HPNE_Kras_day2_sc136


title: HPNE_Kras_day2_sc134


title: HPNE_Kras_day2_sc131


title: HPNE_Kras_day2_sc128


title: HPNE_Kras_day2_sc133


title: HPNE_Kras_day2_sc130


title: HPNE_Kras_day2_sc124


title: HPNE_Kras_day2_sc126


title: HPNE_Kras_day2_sc125


title: HPNE_Kras_day2_sc123


title: HPNE_Kras_day2_sc122


title: HPNE_Kras_day2_sc120


title: HPNE_Kras_day2_sc121


title: HPNE_Kras_day2_sc119


title: HPNE_Kras_day2_sc113


title: HPNE_Kras_day2_sc118


title: HPNE_Kras_day2_sc117


title: HPNE_Kras_day2_sc116


title: HPNE_Kras_day2_sc111


title: HPNE_Kras_day2_sc110


title: HPNE_Kras_day2_sc112


title: HPNE_Kras_day2_sc108


title: HPNE_Kras_day2_sc107


title: HPNE_Kras_day2_sc105


title: HPNE_Kras_day2_sc132


title: HPNE_Kras_day2_sc109


title: HPNE_Kras_day2_sc106


title: HPNE_Kras_day2_sc104


title: HPNE_Kras_day2_sc129


title: HPNE_Kras_day2_sc103


title: HPNE_Kras_day2_sc102


title: HPNE_Kras_day2_sc127


title: HPNE_Kras_day2_sc101


title: HPNE_Kras_day2_sc100


title: HPNE_Kras_day2_sc99


title: HPNE_Kras_day2_sc95


title: HPNE_Kras_day2_sc98


title: HPNE_Kras_day2_sc115


title: HPNE_Kras_day2_sc93


title: HPNE_Kras_day2_sc94


title: HPNE_Kras_day2_sc92


title: HPNE_Kras_day2_sc96


title: HPNE_Kras_day2_sc114


title: HPNE_Kras_day2_sc90


title: HPNE_Kras_day2_sc86


title: HPNE_Kras_day2_sc88


title: HPNE_Kras_day2_sc89


title: HPNE_Kras_day2_sc83


title: HPNE_Kras_day2_sc82


title: HPNE_Kras_day2_sc84


title: HPNE_Kras_day2_sc87


title: HPNE_Kras_day2_sc81


title: HPNE_Kras_day2_sc85


title: HPNE_Kras_day2_sc97


title: HPNE_Kras_day2_sc77


title: HPNE_Kras_day2_sc76


title: HPNE_Kras_day2_sc80


title: HPNE_Kras_day2_sc75


title: HPNE_Kras_day2_sc73


title: HPNE_Kras_day2_sc79


title: HPNE_Kras_day2_sc69


title: HPNE_Kras_day2_sc70


title: HPNE_Kras_day2_sc68


title: HPNE_Kras_day2_sc74


title: HPNE_Kras_day2_sc65


title: HPNE_Kras_day2_sc66


title: HPNE_Kras_day2_sc63


title: HPNE_Kras_day2_sc91


title: HPNE_Kras_day2_sc62


title: HPNE_Kras_day2_sc61


title: HPNE_Kras_day2_sc59


title: HPNE_Kras_day2_sc57


title: HPNE_Kras_day2_sc78


title: HPNE_Kras_day2_sc56


title: HPNE_Kras_day2_sc58


title: HPNE_Kras_day2_sc54


title: HPNE_Kras_day2_sc60


title: HPNE_Kras_day2_sc51


title: HPNE_Kras_day2_sc50


title: HPNE_Kras_day2_sc49


title: HPNE_Kras_day2_sc47


title: HPNE_Kras_day2_sc53


title: HPNE_Kras_day2_sc64


title: HPNE_Kras_day2_sc71


title: HPNE_Kras_day2_sc52


title: HPNE_Kras_day2_sc67


title: HPNE_Kras_day2_sc42


title: HPNE_Kras_day2_sc45


title: HPNE_Kras_day2_sc40


title: HPNE_Kras_day2_sc43


title: HPNE_Kras_day2_sc72


title: HPNE_Kras_day2_sc44


title: HPNE_Kras_day2_sc41


title: HPNE_Kras_day2_sc39


title: HPNE_Kras_day2_sc38


title: HPNE_Kras_day2_sc37


title: HPNE_Kras_day2_sc55


title: HPNE_Kras_day2_sc35


title: HPNE_Kras_day2_sc32


title: HPNE_Kras_day2_sc31


title: HPNE_Kras_day2_sc33


title: HPNE_Kras_day2_sc34


title: HPNE_Kras_day2_sc48


title: HPNE_Kras_day2_sc29


title: HPNE_Kras_day2_sc26


title: HPNE_Kras_day2_sc30


title: HPNE_Kras_day2_sc46


title: HPNE_Kras_day2_sc27


title: HPNE_Kras_day2_sc28


title: HPNE_Kras_day2_sc25


title: HPNE_Kras_day2_sc23


title: HPNE_Kras_day2_sc21


title: HPNE_Kras_day2_sc20


title: HPNE_Kras_day2_sc22


title: HPNE_Kras_day2_sc24


title: HPNE_Kras_day2_sc19


title: HPNE_Kras_day2_sc16


title: HPNE_Kras_day2_sc18


title: HPNE_Kras_day2_sc15


title: HPNE_Kras_day2_sc12


title: HPNE_Kras_day2_sc11


title: HPNE_Kras_day2_sc14


title: HPNE_Kras_day2_sc36


title: HPNE_Kras_day2_sc10


title: HPNE_Kras_day2_sc9


title: HPNE_Kras_day2_sc8


title: HPNE_Kras_day2_sc7


title: HPNE_Kras_day2_sc5


title: HPNE_Kras_day2_sc4


title: HPNE_Kras_day2_sc6


title: HPNE_Kras_day2_sc3


title: HPNE_Kras_day2_sc2


title: HPNE_Kras_day2_sc1


title: HPNE_Kras_day1_sc170

value: KRASG12D overexpression, day1


title: HPNE_Kras_day1_sc169

value: hTERT-HPNE


title: HPNE_Kras_day1_sc168


title: HPNE_Kras_day1_sc171


title: HPNE_Kras_day2_sc17


title: HPNE_Kras_day1_sc164


title: HPNE_Kras_day1_sc166


title: HPNE_Kras_day1_sc161


title: HPNE_Kras_day1_sc163


title: HPNE_Kras_day2_sc13


title: HPNE_Kras_day1_sc165


title: HPNE_Kras_day1_sc157


title: HPNE_Kras_day1_sc158


title: HPNE_Kras_day1_sc159


title: HPNE_Kras_day1_sc156


title: HPNE_Kras_day1_sc162


title: HPNE_Kras_day1_sc154


title: HPNE_Kras_day1_sc155


title: HPNE_Kras_day1_sc151


title: HPNE_Kras_day1_sc150


title: HPNE_Kras_day1_sc152


title: HPNE_Kras_day1_sc160


title: HPNE_Kras_day1_sc149


title: HPNE_Kras_day1_sc148


title: HPNE_Kras_day1_sc147


title: HPNE_Kras_day1_sc167


title: HPNE_Kras_day1_sc144


title: HPNE_Kras_day1_sc146


title: HPNE_Kras_day1_sc143


title: HPNE_Kras_day1_sc140


title: HPNE_Kras_day1_sc142


title: HPNE_Kras_day1_sc139


title: HPNE_Kras_day1_sc138


title: HPNE_Kras_day1_sc141


title: HPNE_Kras_day1_sc137


title: HPNE_Kras_day1_sc133


title: HPNE_Kras_day1_sc134


title: HPNE_Kras_day1_sc136


title: HPNE_Kras_day1_sc135


title: HPNE_Kras_day1_sc131


title: HPNE_Kras_day1_sc153


title: HPNE_Kras_day1_sc132


title: HPNE_Kras_day1_sc128


title: HPNE_Kras_day1_sc129


title: HPNE_Kras_day1_sc130


title: HPNE_Kras_day1_sc127


title: HPNE_Kras_day1_sc126


title: HPNE_Kras_day1_sc145


title: HPNE_Kras_day1_sc121


title: HPNE_Kras_day1_sc123


title: HPNE_Kras_day1_sc125


title: HPNE_Kras_day1_sc122


title: HPNE_Kras_day1_sc120


title: HPNE_Kras_day1_sc119


title: HPNE_Kras_day1_sc124


title: HPNE_Kras_day1_sc118


title: HPNE_Kras_day1_sc116


title: HPNE_Kras_day1_sc117


title: HPNE_Kras_day1_sc113


title: HPNE_Kras_day1_sc114


title: HPNE_Kras_day1_sc115


title: HPNE_Kras_day1_sc109


title: HPNE_Kras_day1_sc110


title: HPNE_Kras_day1_sc111


title: HPNE_Kras_day1_sc108


title: HPNE_Kras_day1_sc107


title: HPNE_Kras_day1_sc112


title: HPNE_Kras_day1_sc102


title: HPNE_Kras_day1_sc105


title: HPNE_Kras_day1_sc106


title: HPNE_Kras_day1_sc104


title: HPNE_Kras_day1_sc103


title: HPNE_Kras_day1_sc101


title: HPNE_Kras_day1_sc99


title: HPNE_Kras_day1_sc100


title: HPNE_Kras_day1_sc98


title: HPNE_Kras_day1_sc97


title: HPNE_Kras_day1_sc96


title: HPNE_Kras_day1_sc94


title: HPNE_Kras_day1_sc95


title: HPNE_Kras_day1_sc90


title: HPNE_Kras_day1_sc91


title: HPNE_Kras_day1_sc92


title: HPNE_Kras_day1_sc88


title: HPNE_Kras_day1_sc87


title: HPNE_Kras_day1_sc86


title: HPNE_Kras_day1_sc84


title: HPNE_Kras_day1_sc85


title: HPNE_Kras_day1_sc83


title: HPNE_Kras_day1_sc82


title: HPNE_Kras_day1_sc81


title: HPNE_Kras_day1_sc77


title: HPNE_Kras_day1_sc76


title: HPNE_Kras_day1_sc80


title: HPNE_Kras_day1_sc75


title: HPNE_Kras_day1_sc78


title: HPNE_Kras_day1_sc71


title: HPNE_Kras_day1_sc72


title: HPNE_Kras_day1_sc68


title: HPNE_Kras_day1_sc74


title: HPNE_Kras_day1_sc73


title: HPNE_Kras_day1_sc93


title: HPNE_Kras_day1_sc69


title: HPNE_Kras_day1_sc89


title: HPNE_Kras_day1_sc66


title: HPNE_Kras_day1_sc67


title: HPNE_Kras_day1_sc64


title: HPNE_Kras_day1_sc65


title: HPNE_Kras_day1_sc60


title: HPNE_Kras_day1_sc61


title: HPNE_Kras_day1_sc59


title: HPNE_Kras_day1_sc56


title: HPNE_Kras_day1_sc57


title: HPNE_Kras_day1_sc54


title: HPNE_Kras_day1_sc79


title: HPNE_Kras_day1_sc55


title: HPNE_Kras_day1_sc53


title: HPNE_Kras_day1_sc52


title: HPNE_Kras_day1_sc50


title: HPNE_Kras_day1_sc51


title: HPNE_Kras_day1_sc70


title: HPNE_Kras_day1_sc49


title: HPNE_Kras_day1_sc46


title: HPNE_Kras_day1_sc42


title: HPNE_Kras_day1_sc48


title: HPNE_Kras_day1_sc47


title: HPNE_Kras_day1_sc63


title: HPNE_Kras_day1_sc43


title: HPNE_Kras_day1_sc62


title: HPNE_Kras_day1_sc40


title: HPNE_Kras_day1_sc38


title: HPNE_Kras_day1_sc45


title: HPNE_Kras_day1_sc37


title: HPNE_Kras_day1_sc44


title: HPNE_Kras_day1_sc36


title: HPNE_Kras_day1_sc41


title: HPNE_Kras_day1_sc39


title: HPNE_Kras_day1_sc35


title: HPNE_Kras_day1_sc58


title: HPNE_Kras_day1_sc34


title: HPNE_Kras_day1_sc33


title: HPNE_Kras_day1_sc31


title: HPNE_Kras_day1_sc30


title: HPNE_Kras_day1_sc28


title: HPNE_Kras_day1_sc27


title: HPNE_Kras_day1_sc29


title: HPNE_Kras_day1_sc23


title: HPNE_Kras_day1_sc24


title: HPNE_Kras_day1_sc25


title: HPNE_Kras_day1_sc26


title: HPNE_Kras_day1_sc21


title: HPNE_Kras_day1_sc20


title: HPNE_Kras_day1_sc17


title: HPNE_Kras_day1_sc15


title: HPNE_Kras_day1_sc19


title: HPNE_Kras_day1_sc18


title: HPNE_Kras_day1_sc12


title: HPNE_Kras_day1_sc11


title: HPNE_Kras_day1_sc16


title: HPNE_Kras_day1_sc8


title: HPNE_Kras_day1_sc9


title: HPNE_Kras_day1_sc10


title: HPNE_Kras_day1_sc14


title: HPNE_Kras_day1_sc6


title: HPNE_Kras_day1_sc5


title: HPNE_Kras_day1_sc32


title: HPNE_Kras_day1_sc7


title: HPNE_Kras_day1_sc3


title: HPNE_Kras_day1_sc4


title: HPNE_Kras_day1_sc1


title: HPNE_Kras_day1_sc2


title: HPNE_Kras_day1_sc22


title: U2OS_sc126

data_processing:
The fastq files of read 1 were mapped to the reference transcriptome by using STAR.
The reads were assigned to exon regions or intron regions by using htseq-count.
The UMI sequences were extracted from read 2 (the first five bases).
The reads with the same UMI were collapsed. The number of UMIs of each gene were counted by exon fragments and intron fragments respectively.
Assembly: hg19, mm10
Supplementary files format and content: Tab-separated UMI count matrix (exon based); Files: HEK293T_exon_UMI_count_matrix.txt, HPNE_exon_UMI_count_matrix.txt, U2OS_exon_UMI_count_matrix.txt
Supplementary files format and content: Tab-separated UMI count matrix (intron based); Files: HEK293T_intron_UMI_count_matrix.txt, HPNE_intron_UMI_count_matrix.txt, U2OS_intron_UMI_count_matrix.txt
Supplementary files format and content: Number of reads mapped to different species, Tab-separated table (for mixed species experiment); File: Mixed_species_summary.txt


title: U2OS_sc125


title: U2OS_sc129


title: U2OS_sc128


title: U2OS_sc127


title: U2OS_sc130


title: U2OS_sc124


title: U2OS_sc123


title: HPNE_Kras_day1_sc13


title: U2OS_sc122


title: U2OS_sc120


title: U2OS_sc121


title: U2OS_sc117


title: U2OS_sc112


title: U2OS_sc119


title: U2OS_sc116


title: U2OS_sc114


title: U2OS_sc113


title: U2OS_sc111


title: U2OS_sc115


title: U2OS_sc108


title: U2OS_sc107


title: U2OS_sc106


title: U2OS_sc105


title: U2OS_sc110


title: U2OS_sc109


title: U2OS_sc104


title: U2OS_sc102


title: U2OS_sc100


title: U2OS_sc96


title: U2OS_sc94


title: U2OS_sc93


title: U2OS_sc95


title: U2OS_sc97


title: U2OS_sc98


title: U2OS_sc118


title: U2OS_sc89


title: U2OS_sc91


title: U2OS_sc87


title: U2OS_sc86


title: U2OS_sc84


title: U2OS_sc85


title: U2OS_sc92


title: U2OS_sc90


title: U2OS_sc81


title: U2OS_sc80


title: U2OS_sc83


title: U2OS_sc77


title: U2OS_sc76


title: U2OS_sc82


title: U2OS_sc75


title: U2OS_sc79


title: U2OS_sc74


title: U2OS_sc101


title: U2OS_sc99


title: U2OS_sc103


title: U2OS_sc73


title: U2OS_sc72


title: U2OS_sc71


title: U2OS_sc66


title: U2OS_sc68


title: U2OS_sc69


title: U2OS_sc67


title: U2OS_sc70


title: U2OS_sc88


title: U2OS_sc64


title: U2OS_sc65


title: U2OS_sc63


title: U2OS_sc61


title: U2OS_sc59


title: U2OS_sc78


title: U2OS_sc57


title: U2OS_sc58


title: U2OS_sc56


title: U2OS_sc55


title: U2OS_sc54


title: U2OS_sc52


title: U2OS_sc50


title: U2OS_sc49


title: U2OS_sc47


title: U2OS_sc46


title: U2OS_sc42


title: U2OS_sc40


title: U2OS_sc41


title: U2OS_sc39


title: U2OS_sc38


title: U2OS_sc53


title: U2OS_sc62


title: U2OS_sc43


title: U2OS_sc37


title: U2OS_sc60


title: U2OS_sc36


title: U2OS_sc32


title: U2OS_sc34


title: U2OS_sc48


title: U2OS_sc44


title: U2OS_sc31


title: U2OS_sc29


title: U2OS_sc30


title: U2OS_sc51


title: U2OS_sc26


title: U2OS_sc27


title: U2OS_sc28


title: U2OS_sc35


title: U2OS_sc23


title: U2OS_sc21


title: U2OS_sc22


title: U2OS_sc45


title: U2OS_sc19


title: U2OS_sc20


title: U2OS_sc17


title: U2OS_sc18


title: U2OS_sc15


title: U2OS_sc16


title: U2OS_sc33


title: U2OS_sc14


title: U2OS_sc13


title: U2OS_sc12


title: U2OS_sc9


title: U2OS_sc11


title: U2OS_sc8


title: U2OS_sc10


title: U2OS_sc4


title: U2OS_sc7


title: U2OS_sc5


title: U2OS_sc1


title: HPNE_sc150


title: U2OS_sc25


title: U2OS_sc2


title: U2OS_sc24


title: HPNE_sc149


title: HPNE_sc146


title: HPNE_sc147


title: HPNE_sc145


title: U2OS_sc3


title: HPNE_sc144


title: HPNE_sc140


title: HPNE_sc142


title: HPNE_sc141


title: HPNE_sc138


title: HPNE_sc139


title: HPNE_sc136


title: HPNE_sc135


title: HPNE_sc137


title: U2OS_sc6


title: HPNE_sc134


title: HPNE_sc133


title: HPNE_sc132


title: HPNE_sc130


title: HPNE_sc128


title: HPNE_sc129


title: HPNE_sc124


title: HPNE_sc127


title: HPNE_sc148


title: HPNE_sc125


title: HPNE_sc123


title: HPNE_sc121


title: HPNE_sc122


title: HPNE_sc118


title: HPNE_sc143


title: HPNE_sc120


title: HPNE_sc117


title: HPNE_sc119


title: HPNE_sc113


title: HPNE_sc115


title: HPNE_sc111


title: HPNE_sc110


title: HPNE_sc114


title: HPNE_sc131


title: HPNE_sc116


title: HPNE_sc107


title: HPNE_sc106


title: HPNE_sc108


title: HPNE_sc105


title: HPNE_sc126


title: HPNE_sc104


title: HPNE_sc102


title: HPNE_sc101


title: HPNE_sc100


title: HPNE_sc112


title: HPNE_sc97


title: HPNE_sc98


title: T108

city: Philadelphia

first: Mathieu

last: Wimmer

state: PA

address: 1701 N 13th Street

institute: Temple University

data_processing:
Evaluating quality of samples with FastQC ver  0.11.9
Remove adapters and unpaired reads using Trimmomatic ver 0.39
Mapping to the geonome by HISAT 2.2.0 release 2/6/2020
Making sorted bam files using SAMtools ver 1.11
Counting number of reads by Stringtie v2.1.2
Finding diffrenetinally expressed genes applying Deseq2 ver 1.28.1
Genome_build: Rnor_6.0
Supplementary_files_format_and_content: tab-delimited text files include FPKM values for each Sample

organism: Rattus norvegicus

source_name: Nucleus accumbens brain tissue

extract_protocol:
Nucleus accumbens tissue was dissected and flash frozen on dry ice. RNA was extracted using trizol reagent followed by the Qiagen micro RNAeasy kit
Library preps were created using the NEBNext Ultra library prep kit for illumina

tag: strain

value: Long Evans

value: Female

tag: agent

value: Cue


title: 550

value: Day 1

value: Sucrose


title: HPNE_sc94


title: T76

value: Day 30


title: HPNE_sc95


title: T72


title: HPNE_sc103


title: HPNE_sc93


title: HPNE_sc92


title: B307


title: HPNE_sc91


title: HPNE_sc109


title: T100


title: T21


title: HPNE_sc90


title: T106


title: HPNE_sc88


title: T50


title: B192


title: B309


title: HPNE_sc89


title: HPNE_sc87


title: HPNE_sc86


title: G59


title: HPNE_sc96


title: HPNE_sc85


title: 617


title: HPNE_sc84


title: T77


title: HPNE_sc83


title: 619


title: HPNE_sc82


title: HPNE_sc81


title: T58


title: 615


title: HPNE_sc80


title: B308


title: HPNE_sc79


title: G58


title: HPNE_sc76


title: 632


title: HPNE_sc77


title: B326


title: HPNE_sc78


title: 545


title: T45


title: HPNE_sc75


title: HPNE_sc73


title: HPNE_sc72


title: 287

value: Male


title: B323


title: 361


title: HPNE_sc71


title: HPNE_sc70


title: 167


title: HPNE_sc69


title: 294


title: Blue12


title: HPNE_sc67


title: HPNE_sc68


title: HPNE_sc99


title: HPNE_sc66


title: Blue10


title: Blue4_Suc


title: HPNE_sc64


title: HPNE_sc65


title: Blue2


title: 394


title: HPNE_sc63


title: HPNE_sc74


title: HPNE_sc61


title: HPNE_sc60


title: 295


title: 290


title: HPNE_sc58


title: 214


title: Blue9


title: HPNE_sc59


title: 291


title: 220


title: HPNE_sc57


title: 380


title: HPNE_sc55


title: HPNE_sc54


title: 379


title: 216


title: HPNE_sc53


title: 135


title: Blue1


title: 422


title: HPNE_sc50


title: 421


title: Blue15

value: Saline


title: Blue17

value: Morphine


title: HPNE_sc49


title: HPNE_sc62


title: HPNE_sc48


title: Blue13


title: Blue14


title: HPNE_sc47


title: HPNE_sc56


title: 487


title: HPNE_sc46


title: 475


title: HPNE_sc44


title: HPNE_sc43


title: 471


title: 484


title: HPNE_sc45


title: 445


title: HPNE_sc41


title: HPNE_sc42


title: 430


title: HPNE_sc52


title: 429


title: HPNE_sc40


title: HPNE_sc39


title: 427


title: HPNE_sc51


title: 413


title: HPNE_sc38


title: HPNE_sc37


title: HPNE_sc36


title: 400


title: HPNE_sc35


title: HPNE_sc33


title: HPNE_sc34


title: HPNE_sc31


title: HPNE_sc32


title: 222


title: 385


title: 224


title: 373


title: HPNE_sc29


title: 399


title: 195


title: 194


title: 206


title: HPNE_sc26


title: HPNE_sc27


title: 426


title: 329


title: HPNE_sc28


title: HPNE_sc25


title: Blue20


title: HPNE_sc24


title: 406


title: 101


title: 560


title: HPNE_sc22


title: HPNE_sc23


title: 321


title: HPNE_sc20


title: HPNE_sc30


title: HPNE_sc21


title: 330


title: 231


title: HPNE_sc16


title: HPNE_sc19


title: Blue16


title: 178


title: HPNE_sc15


title: HPNE_sc17


title: 211


title: 212


title: HPNE_sc18


title: HPNE_sc13


title: 435


title: 511


title: 106


title: HPNE_sc10


title: HPNE_sc11


title: 323


title: 103


title: 512


title: Blue4


title: HPNE_sc9


title: 333


title: HPNE_sc8


title: 451


title: HPNE_sc12


title: 453


title: HPNE_sc7


title: HPNE_sc5


title: 322


title: HPNE_sc4


title: HPNE_sc2


title: snRNA-seq of LAND-treated U87 cells and 3T3 cells with 10x Multiome (DEFND-seq RNA library - second reaction)

first: Peter

middle: A

last: Sims

address: 3960 Broadway, Lasker 203AC

institute: Columbia University

description:
PTO068_2
PTO068_1_2.matrix.txt.gz

data_processing:
snRNA-seq data were processed as described previously [Yuan and Sims, Scientific Reports, 2016]. The code is available at (https://github.com/simslab/DropSeqPipeline8). Briefly, we aligned the transcriptomic reads (read 2) to the human or mouse genome and transcriptome annotation using STAR v2.7.0d [Dobin et al, Bioinformatics, 2013]. For human data sets other than the mixed species experiment, we used GRCh38/Gencode v24. For the mixed species data set, we used a concatenated genome and annotation comprised of GRCh38/Gencode v32 and GRCm38/Gencode vM23. Because we are analyzing nuclei that contain a significant amount of unspliced mRNA, we identified reads that uniquely and strand-specifically aligned to the entire gene body of each gene (including exons, introns, intron-exon junctions, and exon-exon junctions), assigning an address to each aligned read containing the gene name, cell-identifying barcode sequence, and unique molecular identifier (UMI) extracted from read 1. Next, we demultiplexed the resulting table, correcting sequencing errors in the barcodes as described in Yuan and Sims [Yuan and Sims, Scientific Reports, 2016] to produce a count matrix for each sample.
snDNA-seq and snATAC-seq data were processed using a custom pipeline available here (https://github.com/simslab/dna10x). The pipeline attempts to mimic some of the basic data processing procedures that are implemented in the 10x Genomics Cell Ranger software packages for analysis of snATAC-seq and Multiome data, including the formatting of output files. We generated sample-demultiplexed fastq files using the mkfastq command in cellranger-atac v2.0.0 (10x Genomics). We aligned paired-end reads 1 and 2 to the human or mouse genome using bwa mem v0.7.17-r1188 [Li, arXiv, 2013] after removing a standard adapter sequence (CTGTCTCTTATACACATCT) from each read using cutadapt v2.8 [Martin, EMBnet.journal, 17, 1, 2011].  We then extracted all reads with an alignment score that was >90% of the read length and insert size <1 kb. We also implemented an error correction procedure for the cell-identifying barcodes from read 3. Briefly, for cell-identifying barcodes that do not appear in the standard list provided by 10x Genomics, we first determine the frequency falt of each barcode in the standard list in the data set. For each observed barcode sequence that has a Hamming distance of one from a sequence on the standard list, we estimate the posterior probability palt that the barcode deviates from the standard list due to sequencing error using the quality scores for the putatively errant base provided by Illumina or Element palt = falt10-q/10 where q is the quality score. If palt>0.975 for any alternative barcodes, then we replace the errant barcode with the alternative barcode from the standard list with the highest value of palt. Finally, we establish read addresses for each alignment that passes the filter described above comprised of a cell-identifying barcode, chromosome, a fragment start position, a fragment end position and collapse identical fragments. Finally, we sort the fragments by alignment position on the genome and output a table in the format of the “fragments.tsv” file that is typically produced by Cell Ranger.
Assembly: human-only libraries: GRCh38/Gencode v24; human/mouse mixture: GRCm38/Gencode vM23/GRCh38/Gencode v32
Supplementary files format and content: PTO068_1_2.matrix.txt.gz :gzip-compressed, tab-delimited file containing the scRNA-seq count matrix where each row is a gene (labeled by a gene ID and gene symbol) and each column is a cell (with a header containing the cell-identifying barcode and library ID)
Supplementary files format and content: PTO069_*.fragments.tsv.bz2 :bzip2-compressed, tab-delimited file tabulating the alignment position (chromosome, start, end), cell-identifying barcode, and read count for each unique fragment for genomic data (scATAC-seq, scDNA-seq, DEFND-seq)

organism:
Homo sapiens
Mus musculus

source_name: U87-MG, NIH-3T3

growth_protocol: 3T3 cells (ATCC #CRL-1658) and U87 MG cells (ATCC #HTB-14) were cultured in Dulbecco's Modified Eagle's Medium (ATCC #30-2002) supplemented with 10% feline bovine serum (FBS, ThermoFisher # A3160401). Eagle’s Minimum Essential Medium (ATCC #30-2003) was used to culture BJ cells (ATCC CRL-2522). TrypLE Express Enzyme (ThermoFisher #12605010) was used for dissociating cells during cell passages .

extract_protocol:
snATAC-seq: Nuclei were prepared from cryopreserved BJ fibroblasts. Frozen cells were thawed and added to a Dounce homogenizer containing 1 mL of nuclei isolation buffer (NIB: 10 mM TrisHCl pH 7.4, 10 mM NaCl, 3 mM MgCl2, 0.1% Igepal (Millipore Sigma #18896), and 1 x protease inhibitors (Millipore Sigma #118735800001)). The sample was gently homogenized on ice with 5 strokes of the loose pestle and 5 strokes of the tight pestle. The cells were transferred to a conical and 5 mL of PBS (Gibco #10010-031) was added. The sample was spun down at 500 g for 5 minutes, washed with 10 mL of PBS and resuspended in 100 µL of 10x Genomics Nuclei Buffer (10x Genomics, #2000207).  xSDS snDNA-seq: Nuclei that were cross-linked and then treated with sodium dodecyl sulfate (SDS) to remove nucleosomes (xSDS) were prepared following Adey et al. Briefly, BJ fibroblasts were washed with 10 mL of PBS and covered in 3 mL of TrypLE (ThermoFisher #12605028) for 10 minutes at 37 °C. Then 9 mL of media was added, quenching the dissociation, and cells were spun down. The cells were resuspended in 10 mL of media with 406 µL of 37% formaldehyde (Millipore Sigma #252549) and gently rotated at room temperature for 10 minutes. 2.5 M glycine (800 µL) was then added and the suspension was incubated on ice for 5 minutes. Cells were centrifuged at 500 g for 8 minutes and washed with 10 mL of PBS. 5 mL of NIB was added to the pellet and the suspension was incubated for 20 minutes at 4 °C under rotation. Cells were then spun down at 500 g for 5 minutes and washed with 900 µL of NEBuffer 2.1 (New England Biolabs #B7202). The cells were pelleted (500 g for 5 minutes) and resuspended in NEBuffer 2.1 with 12 µL of 20% SDS. The solution was placed in a gentleMACS and vigorously shaken at 42 °C for 30 minutes. 200 µL of 10 % Triton-X (Millipore Sigma #T8787) was added and the cells were again shaken at 42 °C for 30 minutes.  LAND snDNA-seq/DEFND-seq: The LAND protocol for adherent cells using 10x reagents was adapted from the LAND protocol. BJ fibroblasts were first washed with 10 mL of PBS and dissociated with 3 mL of TrypLE for 10 minutes at 37 C. Media (9 mL) was used to quench the dissociation reaction and collect the cells. The cells were spun down (300 g for 5 minutes) and 200 µL of DEFND buffer (175 µL NIB, 10 µL 1 mg/mL protease inhibitor (Millipore Sigma #11429868001), 25 µL 100 mM lithium diiodosalicylate (Millipore Sigma #653-14-5)), was added and incubated on ice for 5 minutes. Immediately following this incubation, 10 mL of nuclei isolation buffer was added and the nuclei were centrifuged at 4 °C for 5 minutes at 500 g. The supernatant was removed and 100 µL of 10x Genomics Nuclei Buffer. A fraction of nuclei was stained with SYBR green and counted on a Countess with a GFP filter set.  GBM Cryopreserved Tissue DEFND-seq: A cryopreserved IDH wildtype Grade IV GBM sample was obtained from excess material collected for clinical purposes from de-identified brain tumor specimens. Nuclei were prepared from this anonymous sample according to XXXXX . Frozen tissue was placed in a Dounce homogenizer containing 1 mL of homogenization buffer (HB: 1 µM DTT, 250 mM sucrose, 25 mM KCl, 5 mM MgCl2, 10 mM tris, 1x protease inhibitor, 0.4 U/µL RNAse, 0.2 U/µL SUPERase In) and subjected to 15 strokes using the loose piston and 15 strokes using the tight piston. The homogenate was divided into 5 volumes and each was strained twice. The filtered homogenate was combined into a tube and centrifuged at 1000 g for 10 minutes at 4 °C. The pellet was resuspended in 1000 µL of HB and strained with 4 strainers (250 µL of homogenate for each strainer). The strained homogenate was again combined into a tube and centrifuged at 1000 g for 10 minutes at 4 °C. The pellet was resuspended in 250 µL of HB to which 250 µL of 50% iodixanol dilution media (IDM: 250 mM sucrose, 150 mM KCl, 30 mM MgCl2, 60 mM tris) was added resulting in a 25% IDM/nuclei suspension. This suspension was carefully layered on top of a tube containing 50% IDM at the bottom and 29% IDM at the surface, and centrifuged at 18,000 g for 23 minutes at 4 C. The nuclei formed a white pellet or sheet in the middle of the tube between the layers. All solution around this pellet was removed – first from the top and then from the bottom, and the pellet was resuspended in 1 mL of chilled PBS and centrifuged (500 g for 5 minutes at 4 °C). The supernatant was removed and the pellet was then treated with DEFND buffer for 5 minutes on ice. Immediately following this incubation, 5 mL of NIB with RNAse inhibitors was added at the nuclei were centrifuged at 500 g for 5 minutes at 4 °C.
DEFND-seq/10x Multiome (snRNA/DNA-seq), snATAC-seq, snDNA-seq
snATAC-seq: Single-cell ATAC libraries were prepared with these nuclei using the 10x Genomics Single Cell ATAC kit (10x Genomics #1000176, #1000162, and #1000212) according to the manufacturer’s protocol. xSDS snDNA-seq: The cells were pelleted (500 g for 5 minutes) and resuspended in 100 µL of 10x Genomics Nuclei Buffer, counted, and tagmented following the Chromium Single Cell ATAC protocol. Tagmented nuclei were loaded onto a 10x Chromoium controller and libraries were prepared according to the Chromimum Single Cell ATAC protocol (10x Genomics #1000176, #1000162, and #1000212). LAND snDNA-seq: Nuclei were then tagmented and prepared for single-cell sequencing with the Chromium Single Cell ATAC kit (10x Genomics #1000176, #1000162, and #1000212) and protocol. DEFND-seq: Nuclei were then tagmented and prepared for single-cell sequencing with the Chromium Single Cell Multiome kit (10x Genomics #1000285, #1000230, #1000215).

value: U87-MG, NIH-3T3

tag: cell type

value: glioma cells (U87), fibroblast (3T3)


title: snRNA-seq of LAND-treated U87 cells and 3T3 cells with 10x Multiome (DEFND-seq RNA library - first reaction)

description:
PTO068_1
PTO068_1_2.matrix.txt.gz


title: HPNE_sc14


title: 233


title: HPNE_sc3


title: Pilot Library, Bin 8

city: Durham

first: Lucia

middle: C.

last: Strader

state: NC

address: 124 Science Drive 3332 French Family Science Center

department: Biology

institute: Duke University

data_processing:
bwa-mem 0.7.17-r1188 was used to perform alignment of reads to the designed DNA fragment library
samtools v1.10 was used to generate sorted BAM files and extract read counts aligned to each fragment
Supplementary files format and content: CSV files with Fragment Name, AD AA sequence, Designed DNA sequence, Number of Reads
Library strategy: Amplicon

organism: Saccharomyces cerevisiae

source_name: MATa TF Library x MATalpha Reporter Strain

extract_protocol:
Sorted cells were grown overnight and then pelleted. Genomic DNA was extracted from cell pellets with YeaStar Genomic DNA Kit (Zymo Research).
Sequencing libraries were generated through three PCR reactions. PCR1 amplified a 600bp fragment that contained the tested fragment from the integrated locus. PCR2 amplified the fragment itself and added phasing and Illumina sequencing adapters. PCR3 completed the Illumina sequencing adapters and added indexes to each sample that were specific for each bin and yeast library tested.

treatment_protocol: Overnight cultures were diluted 1:5 in SC with 1 µM beta-estradiol and grown for 4 hours at 30 °C before sorting on the BC Astrios or BD Aria-II


title: Pilot Library, Bin 7

value: MATa TF Library x MATalpha Reporter Strain


title: HEK293T_B61_M

description: Batch2 (Mixed with 3T3 cells during library construction)


title: Pilot Library, Bin 6


title: HEK293T_B60_M


title: Pilot Library, Bin 5


title: Pilot Library, Bin 4


title: HEK293T_B59_M


title: HEK293T_B58_M


title: Pilot Library, Bin 3


title: HEK293T_B57_M


title: HPNE_sc6


title: HEK293T_B55_M


title: Pilot Library, Bin 2


title: PADI Library 8, Bin 9


title: Pilot Library, Bin 1


title: HEK293T_B54_M


title: HEK293T_B56_M


title: PADI Library 8, Bin 8


title: HEK293T_B53_M


title: PADI Library 8, Bin 7


title: HPNE_sc1


title: HEK293T_B52_M


title: PADI Library 8, Bin 4


title: HEK293T_B50_M


title: PADI Library 8, Bin 5


title: PADI Library 8, Bin 3


title: HEK293T_B49_M


title: HEK293T_B48_M


title: PADI Library 8, Bin 2


title: HEK293T_B47_M


title: HEK293T_B46_M


title: PADI Library 8, Bin 1


title: HEK293T_B45_M


title: PADI Library 8, Bin 11


title: HEK293T_B44_M


title: PADI Library 8, Bin 12


title: PADI Library 8, Bin 10


title: HEK293T_B43_M


title: HuH-7, HBV transfected, PAm6Aseq

data_processing:
fastx toolkit: fastq_quality_filter -Q33| fastx_clipper -Q33 -v -a [index_sequence] -l 15 -c | fastq_to_fasta -Q33
Aligned to the human genome hg19 using Bowtie 1.2.3: bowtie -p 8 -v 1 -a -m 9 --best --strata --chunkmbs 30000
hg19 non-aligning reads aligned to the HBV ayw genome using Bowtie 1.2.3: bowtie -p 8 -m 2 -v 1 -a --norc --best --strata --chunkmbs 30000
Filtered out all reads that lack a TC mutation
Awk script to generate bed file, columns are "chromosome, start, end, score, strand"
Assembly: Our reordered HBV genome is GenBank #J02203.1 with nucleotides 1818-3182(end) forming the first half, and subsequently joined with nucleotides 1-1937 of J02203.1, thus 1818-1937nt of J02203.1 (which covers the viral terminal repeat) is duplicated on both ends of our reordered HBV genome to better represent the HBV native genomic RNA.
Supplementary files format and content: bed files, aligned to the HBV ayw strain genome
Library strategy: PA-m6A-seq

extract_protocol:
PA-m6A-seq (PAR-CLIP done with an m6A RNA targeting antibody)
All samples were processed with the NEB Next small RNA-seq library prep kit for Illumina

value: hepatocyte

value: WT

value: +HBV


title: HEK293T_B41_M


title: HuH-7, HBV transfected, PAm5Cseq


title: HEK293T_B39


title: HEK293T_B51_M


title: HuH-7, HBV transfected, total RNAseq

data_processing:
fastx toolkit: fastq_quality_filter -Q33| fastx_clipper -Q33 -v -a [index_sequence] -l 15 -c | fastq_to_fasta -Q33
Aligned to the human genome hg19 using Bowtie 1.2.3: bowtie -p 8 -v 1 -a -m 9 --best --strata --chunkmbs 30000
hg19 non-aligning reads aligned to the HBV ayw genome using Bowtie 1.2.3: bowtie -p 8 -m 2 -v 1 -a --norc --best --strata --chunkmbs 30000
Awk script to generate bed file, columns are "chromosome, start, end, score, strand"
Assembly: Our reordered HBV genome is GenBank #J02203.1 with nucleotides 1818-3182(end) forming the first half, and subsequently joined with nucleotides 1-1937 of J02203.1, thus 1818-1937nt of J02203.1 (which covers the viral terminal repeat) is duplicated on both ends of our reordered HBV genome to better represent the HBV native genomic RNA.
Supplementary files format and content: bed files, aligned to the HBV ayw strain genome

extract_protocol:
standard RNA seq
All samples were processed with the NEB Next small RNA-seq library prep kit for Illumina


title: PADI Library 8, Bin 6


title: HEK293T_B42_M


title: HuH-7, mock transfected, total RNAseq

value: untreated


title: HuH-7, mock transfected, PAm5Cseq


title: PADI Library Replicate 3B, Bin 9

source_name: MATa TF Library x MAT{alpha} Reporter Strain


title: HEK293T_B36


title: myofibroblast, WT, treated

city: Singapore

first: Jing

last: Guo

state: State...

address: 8 Collage Road, DUKE-NUS Medical School, level 5

department: Center for Computational Biology

country: Singapore

institute: Duke-NUS Medical School

data_processing:
Libraries were sequenced by illumine sequencer Hiseq 4000 of 150 bp pair-end reads.
FASTQ files were mapped to mouse reference genome GRCm38 using STAR aligner. PRC duplicated reads were removed by Picard MarkDuplicates function.
Peak calling was performed by MACS2 callpeak function using the following parameters: -qvalue 0.001, --keep-dup auto, and --call-summits.
Assembly: mm10
Supplementary files format and content: bed file

source_name: Primary renal myofibroblasts

extract_protocol:
Chromatin immuno-precipitation (ChIP) assay was performed using Magnetic ChIP Kit (Pierce) with anti-WWP2 antibody (#A302-936A, Bethyl Laboratories). Briefly, P2 WT renal fibroblasts were grown for 80-90% confluence. After treatment with TGFβ1 (5ng/ml) for 24 h, cells were harvested by trypsinisation. DNA and proteins in the cells (~106 each sample) were cross-linked using 1% (v/v) formaldehyde and then sonicated in lysis buffer to obtain 200 bp–500 bp long DNA fragments. Supernatant was incubated with control IgG or WWP2 antibody beads at 4°C, or kept as input references.Reverse-crosslinking and purification of DNA was performed.
ChIP-seq libraries were constructed and sequenced using Illumina HiSeq 4000 sequencer, resulting in paired-end FASTQ files containing sequence reads of 150bp length

value: Primary renal myofibroblasts

value: control

tag: antibody


title: HEK293T_B35


title: HEK293T_B34


title: PADI Library Replicate 3B, Bin 7

value: MATa TF Library x MAT{alpha} Reporter Strain


title: PADI Library Replicate 3B, Bin 8


title: HEK293T_B33


title: PADI Library Replicate 3B, Bin 5


title: HEK293T_B32


title: HEK293T_B31


title: PADI Library Replicate 3B, Bin 4


title: HEK293T_B30


title: HEK293T_B29


title: HEK293T_B40


title: HuH-7, mock transfected, PAm6Aseq


title: PADI Library Replicate 3B, Bin 2


title: HEK293T_B28


title: HEK293T_B27


title: PADI Library Replicate 3B, Bin 12


title: HEK293T_B26


title: HEK293T_B38


title: PADI Library Replicate 3B, Bin 11


title: HEK293T_B37


title: PADI Library Replicate 3B, Bin 10


title: HEK293T_B25


title: PADI Library Replicate 3B, Bin 1


title: HEK293T_B24


title: mCherry-Only Library, Bin 6


title: mCherry-Only Library, Bin 5


title: HEK293T_B22


title: PADI Library Replicate 3B, Bin 6


title: mCherry-Only Library, Bin 3


title: mCherry-Only Library, Bin 4


title: HEK293T_B20


title: mCherry-Only Library, Bin 2


title: PADI Library Replicate 3B, Bin 3


title: GFP-Only Library, Bin 6


title: GFP-Only Library, Bin 5


title: HEK293T_B17


title: HEK293T_B16


title: HEK293T_B19


title: mCherry-Only Library, Bin 1


title: HEK293T_B15


title: GFP-Only Library, Bin 4


title: GFP-Only Library, Bin 1


title: HEK293T_B14


title: GFP-Only Library, Bin 2


title: HEK293T_B12


title: PADI Library 9, Bin 9


title: HEK293T_B13


title: GFP-Only Library, Bin 3


title: HEK293T_B23


title: HEK293T_B10


title: HEK293T_B21


title: HEK293T_B09


title: PADI Library 9, Bin 7


title: PADI Library 9, Bin 6


title: PADI Library 9, Bin 5


title: PADI Library 9, Bin 4


title: PADI Library 9, Bin 3


title: PADI Library 9, Bin 8


title: HEK293T_B08


title: HEK293T_B18


title: HEK293T_B04


title: HEK293T_B06


title: HEK293T_B03


title: PADI Library 9, Bin 1


title: HEK293T_B02


title: PADI Library 9, Bin 2


title: HEK293T_B11


title: HEK293T_B05


title: HEK293T_B01


title: PADI Library 9, Bin 12


title: PADI Library 7, Bin 9


title: HEK293T_A82


title: HEK293T_A80


title: PADI Library 7, Bin 7


title: PADI Library 7, Bin 8


title: HEK293T_A81


title: PADI Library 9, Bin 10


title: HEK293T_A79


title: PADI Library 7, Bin 6


title: PADI Library 9, Bin 11


title: HEK293T_A78


title: HEK293T_A77


title: HEK293T_B07


title: HEK293T_A76


title: PADI Library 7, Bin 3


title: HEK293T_A75


title: PADI Library 7, Bin 4


title: PADI Library 7, Bin 2


title: HEK293T_A74


title: PADI Library 7, Bin 1


title: PADI Library 7, Bin 12


title: HEK293T_A73


title: HEK293T_A72


title: HEK293T_A71


title: PADI Library 7, Bin 11


title: PADI Library 6, Bin 9


title: HEK293T_A69


title: HEK293T_A70


title: PADI Library 6, Bin 8


title: HEK293T_A68


title: PADI Library 7, Bin 10


title: HEK293T_A67


title: PADI Library 7, Bin 5


title: HEK293T_A65


title: PADI Library 6, Bin 7


title: HEK293T_A64


title: PADI Library 6, Bin 3


title: HEK293T_A66


title: HEK293T_A63


title: PADI Library 6, Bin 2


title: PADI Library 6, Bin 4


title: PADI Library 6, Bin 6


title: HEK293T_A62


title: PADI Library 6, Bin 1


title: HEK293T_A61


title: HEK293T_A60


title: PADI Library 6, Bin 11


title: HEK293T_A59


title: PADI Library 6, Bin 10


title: HEK293T_A58


title: PADI Library 6, Bin 12


title: PADI Library 5, Bin 9


title: HEK293T_A57


title: HEK293T_A56


title: PADI Library 5, Bin 8


title: PADI Library 6, Bin 5


title: PADI Library 5, Bin 6


title: PADI Library 5, Bin 5


title: PADI Library 5, Bin 7


title: HEK293T_A55


title: PADI Library 5, Bin 4


title: HEK293T_A52


title: PADI Library 5, Bin 3


title: PADI Library 5, Bin 2


title: HEK293T_A53


title: HEK293T_A51


title: HEK293T_A50


title: HEK293T_A48


title: HEK293T_A49


title: PADI Library 5, Bin 12


title: PADI Library 5, Bin 10


title: HEK293T_A47


title: PADI Library 5, Bin 11


title: HEK293T_A46


title: HEK293T_A45


title: PADI Library 4, Bin 9


title: PADI Library 4, Bin 8


title: HEK293T_A43


title: PADI Library 4, Bin 7


title: HEK293T_A54


title: HEK293T_A40


title: PADI Library 4, Bin 5


title: HEK293T_A42


title: HEK293T_A41


title: PADI Library 4, Bin 3


title: PADI Library 5, Bin 1


title: PADI Library 4, Bin 6


title: HEK293T_A39


title: PADI Library 4, Bin 2


title: HEK293T_A37


title: PADI Library 4, Bin 4


title: HEK293T_A36


title: HEK293T_A35


title: PADI Library 4, Bin 12


title: PADI Library 4, Bin 10


title: PADI Library 4, Bin 11


title: HEK293T_A34


title: PADI Library 3, Bin 8


title: PADI Library 3, Bin 9


title: HEK293T_A44


title: HEK293T_A33


title: HEK293T_A32


title: PADI Library 3, Bin 6


title: HEK293T_A31


title: PADI Library 3, Bin 5


title: HEK293T_A30


title: PADI Library 3, Bin 4


title: PADI Library 4, Bin 1


title: HEK293T_A28


title: PADI Library 3, Bin 3


title: HEK293T_A38


title: PADI Library 3, Bin 1


title: HEK293T_A26


title: HEK293T_A29


title: HEK293T_A27


title: PADI Library 3, Bin 11


title: HEK293T_A24


title: PADI Library 3, Bin 2


title: HEK293T_A23